Publications by authors named "Sunish K Sehgal"

21 Publications

  • Page 1 of 1

Multi-Trait Multi-Environment Genomic Prediction of Agronomic Traits in Advanced Breeding Lines of Winter Wheat.

Front Plant Sci 2021 18;12:709545. Epub 2021 Aug 18.

Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States.

Genomic prediction is a promising approach for accelerating the genetic gain of complex traits in wheat breeding. However, increasing the prediction accuracy (PA) of genomic prediction (GP) models remains a challenge in the successful implementation of this approach. Multivariate models have shown promise when evaluated using diverse panels of unrelated accessions; however, limited information is available on their performance in advanced breeding trials. Here, we used multivariate GP models to predict multiple agronomic traits using 314 advanced and elite breeding lines of winter wheat evaluated in 10 site-year environments. We evaluated a multi-trait (MT) model with two cross-validation schemes representing different breeding scenarios (CV1, prediction of completely unphenotyped lines; and CV2, prediction of partially phenotyped lines for correlated traits). Moreover, extensive data from multi-environment trials (METs) were used to cross-validate a Bayesian multi-trait multi-environment (MTME) model that integrates the analysis of multiple-traits, such as G × E interaction. The MT-CV2 model outperformed all the other models for predicting grain yield with significant improvement in PA over the single-trait (ST-CV1) model. The MTME model performed better for all traits, with average improvement over the ST-CV1 reaching up to 19, 71, 17, 48, and 51% for grain yield, grain protein content, test weight, plant height, and days to heading, respectively. Overall, the empirical analyses elucidate the potential of both the MT-CV2 and MTME models when advanced breeding lines are used as a training population to predict related preliminary breeding lines. Further, we evaluated the practical application of the MTME model in the breeding program to reduce phenotyping cost using a sparse testing design. This showed that complementing METs with GP can substantially enhance resource efficiency. Our results demonstrate that multivariate GS models have a great potential in implementing GS in breeding programs.
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http://dx.doi.org/10.3389/fpls.2021.709545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8416538PMC
August 2021

Genome-wide association analysis permits characterization of Stagonospora nodorum blotch (SNB) resistance in hard winter wheat.

Sci Rep 2021 06 15;11(1):12570. Epub 2021 Jun 15.

Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.

Stagonospora nodorum blotch (SNB) is an economically important wheat disease caused by the necrotrophic fungus Parastagonospora nodorum. SNB resistance in wheat is controlled by several quantitative trait loci (QTLs). Thus, identifying novel resistance/susceptibility QTLs is crucial for continuous improvement of the SNB resistance. Here, the hard winter wheat association mapping panel (HWWAMP) comprising accessions from breeding programs in the Great Plains region of the US, was evaluated for SNB resistance and necrotrophic effectors (NEs) sensitivity at the seedling stage. A genome-wide association study (GWAS) was performed to identify single-nucleotide polymorphism (SNP) markers associated with SNB resistance and effectors sensitivity. We found seven significant associations for SNB resistance/susceptibility distributed over chromosomes 1B, 2AL, 2DS, 4AL, 5BL, 6BS, and 7AL. Two new QTLs for SNB resistance/susceptibility at the seedling stage were identified on chromosomes 6BS and 7AL, whereas five QTLs previously reported in diverse germplasms were validated. Allele stacking analysis at seven QTLs explained the additive and complex nature of SNB resistance. We identified accessions ('Pioneer-2180' and 'Shocker') with favorable alleles at five of the seven identified loci, exhibiting a high level of resistance against SNB. Further, GWAS for sensitivity to NEs uncovered significant associations for SnToxA and SnTox3, co-locating with previously identified host sensitivity genes (Tsn1 and Snn3). Candidate region analysis for SNB resistance revealed 35 genes of putative interest with plant defense response-related functions. The QTLs identified and validated in this study could be easily employed in breeding programs using the associated markers to enhance the SNB resistance in hard winter wheat.
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http://dx.doi.org/10.1038/s41598-021-91515-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8206080PMC
June 2021

Development of Novel Wheat-Aegilops longissima 3Sl Translocations Conferring Powdery Mildew Resistance and Specific Molecular Markers for Chromosome 3Sl.

Plant Dis 2021 Mar 31. Epub 2021 Mar 31.

Henan Agricultural University, 70573, College of Life Sciences, Zhengzhou, Henan, China;

Powdery mildew of wheat, caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease of wheat. Cultivation of resistant varieties is the most cost-effective disease management strategy. Previous studies reported that chromosome 3Sl#2 present in Chinese Spring (CS)-Aegilops longissima 3Sl#2(3B) disomic substitution line TA3575 conferred resistance to powdery mildew. In this study, we further located the powdery mildew resistance gene(s) to the short arm of chromosome 3Sl#2 (3Sl#2S) by evaluating for Bgt-resistance of newly developed CS-Ae. longissima 3Sl#2 translocation lines. Meanwhile, TA7545, a previously designated CS-Ae. longissima 3Sl#3 disomic addition line, was re-identified as an isochromosome 3Sl#3S addition line and evaluated to confer resistance to powdery mildew, thus locating the resistance gene(s) to the short arm of chromosome 3Sl#3 (3Sl#3S). Based on transcriptome sequences of TA3575, ten novel chromosome 3SlS-specific markers were developed, of which, five could be used to distinguish between 3Sl#2S and 3Sl#3S derived from Ae. longissima accessions TL20 and TA1910 (TAM4), and the remaining five could identify both 3Sl#2S and 3Sl#3S. Besides, CL897, one of five markers specific to both 3Sl#2S and 3Sl#3S, could be used to detect Pm13 located at chromosome 3Sl#1S from Ae. longissima accession TL01 in diverse wheat genetic backgrounds. The powdery mildew resistance genes on chromosomes 3Sl#2S and 3Sl#3S, the CS-Ae. longissima 3Sl#2 translocation lines, and the 3SlS-specific markers developed in this study will provide new germplasm resources for powdery mildew resistance breeding and facilitate the transfer of Bgt-resistance genes into common wheat.
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http://dx.doi.org/10.1094/PDIS-12-20-2691-REDOI Listing
March 2021

Artificial selection in breeding extensively enriched a functional allelic variation in TaPHS1 for pre-harvest sprouting resistance in wheat.

Theor Appl Genet 2021 Jan 17;134(1):339-350. Epub 2020 Oct 17.

Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.

Pre-harvest sprouting (PHS) causes significant losses in wheat yield and quality worldwide. Previously, we cloned a PHS resistance gene, TaPHS1, and identified two causal mutations for reduced seed dormancy (SD) and increased PHS susceptibility. Here we identified a novel allelic variation of C to T transition in 3'-UTR of TaPHS1, which associated with reduced SD and PHS resistance. The T allele occurred in wild wheat progenitors and was likely the earliest functional mutation in TaPHS1 for PHS susceptibility. Allele frequency analysis revealed low frequency of the T allele in wild diploid and tetraploid wheat progenitors, but very high frequency in modern wheat cultivars and breeding lines, indicating that artificial selection quickly enriched the T allele during modern breeding. The T allele was significantly associated with short SD in both T. aestivum and T. durum, the two most cultivated species of wheat. This variation together with previously reported functional sequence variations co-regulated TaPHS1 expression levels and PHS resistance in different germplasms. Haplotype analysis of the four functional variations identified the best PHS resistance haplotype of TaPHS1. The resistance haplotype can be used in marker-assisted selection to transfer TaPHS1 to new wheat cultivars.
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http://dx.doi.org/10.1007/s00122-020-03700-2DOI Listing
January 2021

Physical Mapping of , a Powdery Mildew Resistance Gene Derived from .

Int J Mol Sci 2020 Jan 3;21(1). Epub 2020 Jan 3.

National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.

Powdery mildew caused by f. sp. () is one of many severe diseases that threaten bread wheat ( L.) yield and quality worldwide. The discovery and deployment of powdery mildew resistance genes () can prevent this disease epidemic in wheat. In a previous study, we transferred the powdery mildew resistance gene from into common wheat and cytogenetically mapped the gene in a chromosome region with the fraction length (FL) 0.75-0.87, which represents 12% segment of the long arm of chromosome 2S#1. In this study, we performed RNA-seq using RNA extracted from leaf samples of three infected and mock-infected wheat-. 2S#1 introgression lines at 0, 12, 24, and 48 h after inoculation with isolates. Then we designed 79 molecular markers based on transcriptome sequences and physically mapped them to . chromosome 2S#1- in seven intervals. We used these markers to identify 46 wheat-. 2S#1 recombinants induced by , a deletion mutant of pairing homologous () genes. After analyzing the 46 -induced 2S#1L recombinants in the region where is located with different -responses, we physically mapped gene on the long arm of 2S#1 in a 5.13 Mb genomic region, which was flanked by markers (773.72 Mb) and (778.85 Mb). By comparative synteny analysis of the corresponding region on chromosome 2B in Chinese Spring ( L.) with other model species, we identified ten genes that are putative plant defense-related (R) genes which includes six coiled-coil nucleotide-binding site-leucine-rich repeat (CNL), three nucleotide-binding site-leucine-rich repeat (NL) and a leucine-rich receptor-like repeat (RLP) encoding proteins. This study will lay a foundation for cloning of , and benefit the understanding of interactions between resistance genes of wheat and powdery mildew pathogens.
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http://dx.doi.org/10.3390/ijms21010322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6982159PMC
January 2020

Mining and genomic characterization of resistance to tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat landraces.

BMC Plant Biol 2019 Nov 8;19(1):480. Epub 2019 Nov 8.

Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, 57007, USA.

Background: In the late 1920s, A. E. Watkins collected about 7000 landrace cultivars (LCs) of bread wheat (Triticum aestivum L.) from 32 different countries around the world. Among which 826 LCs remain viable and could be a valuable source of superior/favorable alleles to enhance disease resistance in wheat. In the present study, a core set of 121 LCs, which captures the majority of the genetic diversity of Watkins collection, was evaluated for identifying novel sources of resistance against tan spot, Stagonospora nodorum blotch (SNB), and Fusarium Head Blight (FHB).

Results: A diverse response was observed in 121 LCs for all three diseases. The majority of LCs were moderately susceptible to susceptible to tan spot Ptr race 1 (84%) and FHB (96%) whereas a large number of LCs were resistant or moderately resistant against tan spot Ptr race 5 (95%) and SNB (54%). Thirteen LCs were identified in this study could be a valuable source for multiple resistance to tan spot Ptr races 1 and 5, and SNB, and another five LCs could be a potential source for FHB resistance. GWAS analysis was carried out using disease phenotyping score and 8807 SNPs data of 118 LCs, which identified 30 significant marker-trait associations (MTAs) with -log10 (p-value) > 3.0. Ten, five, and five genomic regions were found to be associated with resistance to tan spot Ptr race 1, race 5, and SNB, respectively in this study. In addition to Tsn1, several novel genomic regions Q.Ts1.sdsu-4BS and Q.Ts1.sdsu-5BS (tan spot Ptr race 1) and Q.Ts5.sdsu-1BL, Q.Ts5.sdsu-2DL, Q.Ts5.sdsu-3AL, and Q.Ts5.sdsu-6BL (tan spot Ptr race 5) were also identified. Our results indicate that these putative genomic regions contain several genes that play an important role in plant defense mechanisms.

Conclusion: Our results suggest the existence of valuable resistant alleles against leaf spot diseases in Watkins LCs. The single-nucleotide polymorphism (SNP) markers linked to the quantitative trait loci (QTLs) for tan spot and SNB resistance along with LCs harboring multiple disease resistance could be useful for future wheat breeding.
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http://dx.doi.org/10.1186/s12870-019-2093-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839225PMC
November 2019

Molecular characterization of bacterial leaf streak resistance in hard winter wheat.

PeerJ 2019 15;7:e7276. Epub 2019 Jul 15.

Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA.

Bacterial leaf streak (BLS) caused by is one of the major bacterial diseases threatening wheat production in the United States Northern Great Plains (NGP) region. It is a sporadic but widespread wheat disease that can cause significant loss in grain yield and quality. Identification and characterization of genomic regions in wheat that confer resistance to BLS will help track resistance genes/QTLs in future wheat breeding. In this study, we evaluated a hard winter wheat association mapping panel (HWWAMP) containing 299 hard winter wheat lines from the US hard winter wheat growing region for their reactions to BLS. We observed a range of BLS responses among the lines, importantly, we identified ten genotypes that showed a resistant reaction both in greenhouse and field evaluation. -Genome-wide association analysis with 15,990 SNPs was conducted using an exponentially compressed mixed linear model. Five genomic regions ( < 0.001) that regulate the resistance to BLS were identified on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS. The QTLs , , , and explain a total of 42% of the variation. In silico analysis of sequences in the candidate regions on chromosomes 1AL, 1BS, 3AL, 4AL, and 7AS identified 10, 25, 22, eight, and nine genes, respectively with known plant defense-related functions. Comparative analysis with rice showed two syntenic regions in rice that harbor genes for bacterial leaf streak resistance. The ten BLS resistant genotypes and SNP markers linked to the QTLs identified in our study could facilitate breeding for BLS resistance in winter wheat.
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http://dx.doi.org/10.7717/peerj.7276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637926PMC
July 2019

Fine Mapping of the Wheat Leaf Rust Resistance Gene .

Int J Mol Sci 2019 May 17;20(10). Epub 2019 May 17.

Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD 57006, USA.

Leaf rust caused by Eriks is one of the most problematic diseases of wheat throughout the world. The gene confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported to be both recessive and dominant in hexaploid wheat; however, in diploid (TA2450), we found to be dominant by studying segregation in two independent F and their F populations. We further fine-mapped in hexaploid wheat using a KS93U50/Morocco F recombinant inbred line (RIL) population to a 3.7 cM genetic interval flanked by markers and . The 3.7 cM region physically corresponds to a 3.16 Mb genomic region on chromosome 1DS based on the Chinese Spring reference genome (RefSeq v.1.1) and a 3.5 Mb genomic interval on chromosome 1 in the reference genome. This region includes nine nucleotide-binding domain leucine-rich repeat (NLR) genes in wheat and seven in , respectively, and these are the likely candidates for . Furthermore, we developed two kompetitive allele-specific polymorphism (KASP) markers ( and ) flanking to facilitate marker-assisted selection for rust resistance in wheat breeding programs.
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http://dx.doi.org/10.3390/ijms20102445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567072PMC
May 2019

Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye.

PLoS One 2019 28;14(3):e0214519. Epub 2019 Mar 28.

Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States of America.

Rye (Secale cereale L.) is known for its wide adaptation due to its ability to tolerate harsh environments in semiarid areas. To assess the diversity in rye we genotyped a panel of 178 geographically diverse accessions of four Secale sp. from U.S. National Small Grains Collection using 4,037 high-quality SNPs (single nucleotide polymorphisms) developed by genotyping-by-sequencing (GBS). PCA and STRUCTURE analysis revealed three major clusters that separate S. cereale L. from S. strictum and S. sylvestre, however, genetic clusters did not correlate with geographic origins and growth habit (spring/winter). The panel was evaluated for response to Pyrenophora tritici-repentis race 5 (PTR race 5) and nearly 59% accessions showed resistance or moderate resistance. Genome-wide association study (GWAS) was performed on S. cereale subsp. cereale using the 4,037 high-quality SNPs. Two QTLs (QTs.sdsu-5R and QTs.sdsu-2R) on chromosomes 5R and 2R were identified conferring resistance to PTR race 5 (p < 0.001) that explained 13.1% and 11.6% of the phenotypic variation, respectively. Comparative analysis showed a high degree of synteny between rye and wheat with known rearrangements as expected. QTs.sdsu-2R was mapped in the genomic region corresponding to wheat chromosome group 2 and QTs.sdsu-5R was mapped to a small terminal region on chromosome 4BL. Based on the genetic diversity, a set of 32 accessions was identified to represents more than 99% of the allelic diversity with polymorphic information content (PIC) of 0.25. This set can be utilized for genetic characterization of useful traits and genetic improvement of rye, triticale, and wheat.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214519PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438500PMC
December 2019

Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat.

Front Plant Sci 2018 6;9:926. Epub 2018 Jul 6.

Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States.

Spot blotch (SB) caused by (anamorph: ) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs ( = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, (SNP: Kukri_c31121_1460, = 4%), (SNP: Excalibur_c46082_440, = 4%), 1 (SNP: IWA8475, = 5.5%), (SNP: Excalibur_rep_c79414_306, = 4%), (SNP: Kukri_rep_c104877_2166, = 6%), and (SNP: TA005844-0160, = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (, 1, and ) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
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http://dx.doi.org/10.3389/fpls.2018.00926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043670PMC
July 2018

Reaction of Global Collection of Rye ( L.) to Tan Spot and Races in South Dakota.

Plant Pathol J 2017 Jun 1;33(3):229-237. Epub 2017 Jun 1.

Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007, USA.

Rye ( L.) serves as an alternative host of () the cause of tan spot on wheat. Rye is cultivated as a forage or cover crop and overlaps with a significant portion of wheat acreage in the U.S. northern Great Plains; however, it is not known whether the rye crop influences the evolution of races. We evaluated a global collection of 211 rye accessions against tan spot and assessed the diversity in population on rye in South Dakota. All the rye genotypes were inoculated with races 1 and 5, and infiltrated with Ptr ToxA and Ptr ToxB, at seedling stage. We observed 21% of the genotypes exhibited susceptibility to race 1, whereas, 39% were susceptible to race 5. All 211 accessions were insensitive to both the Ptr toxins. It indicates that though rye exhibits diversity in reaction to tan spot, it lacks and sensitivity genes. This suggests that unknown toxins or other factors can lead to establishment in rye. We characterized the race structure of 103 isolates recovered from rye in South Dakota. Only 22% of the isolates amplified gene and were identified as race 1 based on their phenotypic reaction on the differential set. The remaining 80 isolates were noted to be race 4. Our results show that races 1 and 4 are prevalent on rye in South Dakota with a higher frequency of race 4, suggesting a minimal role of rye in the disease epidemiology.
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http://dx.doi.org/10.5423/PPJ.OA.12.2016.0265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5461042PMC
June 2017

Fine mapping of the stem rust resistance gene SrTA10187.

Theor Appl Genet 2016 Dec 31;129(12):2369-2378. Epub 2016 Aug 31.

Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue Street, Room A286, East Lansing, MI, 48824, USA.

Key Message: SrTA10187 was fine-mapped to a 1.1 cM interval, candidate genes were identified in the region of interest, and molecular markers were developed for marker-assisted selection and Sr gene pyramiding. Stem rust (Puccinia graminis f. sp. tritici, Pgt) races belonging to the Ug99 (TTKSK) race group pose a serious threat to global wheat (Triticum aestivum L.) production. To improve Pgt host resistance, the Ug99-effective resistance gene SrTA10187 previously identified in Aegilops tauschii Coss. was introgressed into wheat, and mapped to the short arm of wheat chromosome 6D. In this study, high-resolution mapping of SrTA10187 was done using a population of 1,060 plants. Pgt resistance was screened using race QFCSC. PCR-based SNP and STS markers were developed from genotyping-by-sequencing tags and SNP sequences available in online databases. SrTA10187 segregated as expected in a 3:1 ratio of resistant to susceptible individuals in three out of six BCF families, and was fine-mapped to a 1.1 cM region on wheat chromosome 6DS. Marker context sequence was aligned to the reference Ae. tauschii genome to identify the physical region encompassing SrTA10187. Due to the size of the corresponding region, candidate disease resistance genes could not be identified with confidence. Comparisons with the Ae. tauschii genetic map developed by Luo et al. (PNAS 110(19):7940-7945, 2013) enabled identification of a discrete genetic locus and a BAC minimum tiling path of the region spanning SrTA10187. Annotation of pooled BAC library sequences led to the identification of candidate genes in the region of interest-including a single NB-ARC-LRR gene. The shorter genetic interval and flanking KASP™ and STS markers developed in this study will facilitate marker-assisted selection, gene pyramiding, and positional cloning of SrTA10187.
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http://dx.doi.org/10.1007/s00122-016-2776-1DOI Listing
December 2016

Structure and Stability of Telocentric Chromosomes in Wheat.

PLoS One 2015 18;10(9):e0137747. Epub 2015 Sep 18.

Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, United States of America.

In most eukaryotes, centromeres assemble at a single location per chromosome. Naturally occurring telocentric chromosomes (telosomes) with a terminal centromere are rare but do exist. Telosomes arise through misdivision of centromeres in normal chromosomes, and their cytological stability depends on the structure of their kinetochores. The instability of telosomes may be attributed to the relative centromere size and the degree of completeness of their kinetochore. Here we test this hypothesis by analyzing the cytogenetic structure of wheat telosomes. We used a population of 80 telosomes arising from the misdivision of the 21 chromosomes of wheat that have shown stable inheritance over many generations. We analyzed centromere size by probing with the centromere-specific histone H3 variant, CENH3. Comparing the signal intensity for CENH3 between the intact chromosome and derived telosomes showed that the telosomes had approximately half the signal intensity compared to that of normal chromosomes. Immunofluorescence of CENH3 in a wheat stock with 28 telosomes revealed that none of the telosomes received a complete CENH3 domain. Some of the telosomes lacked centromere specific retrotransposons of wheat in the CENH3 domain, indicating that the stability of telosomes depends on the presence of CENH3 chromatin and not on the presence of CRW repeats. In addition to providing evidence for centromere shift, we also observed chromosomal aberrations including inversions and deletions in the short arm telosomes of double ditelosomic 1D and 6D stocks. The role of centromere-flanking, pericentromeric heterochromatin in mitosis is discussed with respect to genome/chromosome integrity.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137747PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4575054PMC
May 2016

Independent mis-splicing mutations in TaPHS1 causing loss of preharvest sprouting (PHS) resistance during wheat domestication.

New Phytol 2015 Nov 10;208(3):928-35. Epub 2015 Aug 10.

Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.

Preharvest sprouting (PHS) is one of the major constraints of wheat production in areas where prolonged rainfall occurs during harvest. TaPHS1 is a gene that regulates PHS resistance on chromosome 3A of wheat, and two causal mutations in the positions +646 and +666 of the TaPHS1 coding region result in wheat PHS susceptibility. Three competitive allele-specific PCR (KASP) markers were developed based on the two mutations in the coding region and one in the promoter region and validated in 82 wheat cultivars with known genotypes. These markers can be used to transfer TaPHS1 in breeding through marker-assisted selection. Screening of 327 accessions of wheat A genome progenitors using the three KASP markers identified different haplotypes in both diploid and tetraploid wheats. Only one Triticum monococcum accession, however, carries both causal mutations in the TaPHS1 coding region and shows PHS susceptibility. Five of 249 common wheat landraces collected from the Fertile Crescent and surrounding areas carried the mutation (C) in the promoter (-222), and one landrace carries both the causal mutations in the TaPHS1 coding region, indicating that the mis-splicing (+646) mutation occurred during common wheat domestication. PHS assay of wheat progenitor accessions demonstrated that the wild-types were highly PHS-resistant, whereas the domesticated type showed increased PHS susceptibility. The mis-splicing TaPHS1 mutation for PHS susceptibility was involved in wheat domestication and might arise independently between T. monococcum and Triticum aestivum.
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http://dx.doi.org/10.1111/nph.13489DOI Listing
November 2015

Chromosome engineering, mapping, and transferring of resistance to Fusarium head blight disease from Elymus tsukushiensis into wheat.

Theor Appl Genet 2015 Jun 1;128(6):1019-27. Epub 2015 Mar 1.

Department of Plant Pathology, Wheat Genetics Resource Center, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA.

Key Message: This manuscript describes the transfer and molecular cytogenetic characterization of a novel source of Fusarium head blight resistance in wheat. Fusarium head blight (FHB) caused by the fungus Fusarium graminearum Schwabe [telomorph = Gibberella zeae (Schwein. Fr.) Petch] is an important disease of bread wheat, Triticum aestivum L. (2n = 6x = 42, AABBDD) worldwide. Wheat has limited resistance to FHB controlled by many loci and new sources of resistance are urgently needed. The perennial grass Elymus tsukushiensis thrives in the warm and humid regions of China and Japan and is immune to FHB. Here, we report the transfer and mapping of a major gene Fhb6 from E. tsukushiensis to wheat. Fhb6 was mapped to the subterminal region in the short arm of chromosome 1E(ts)#1S of E. tsukushiensis. Chromosome engineering was used to replace corresponding homoeologous region of chromosome 1AS of wheat with the Fhb6 associated chromatin derived from 1E(ts)#1S of E. tsukushiensis. Fhb6 appears to be new locus for wheat as previous studies have not detected any FHB resistance QTL in this chromosome region. Plant progenies homozygous for Fhb6 had a disease severity rating of 7 % compared to 35 % for the null progenies. Fhb6 has been tagged with molecular markers for marker-assisted breeding and pyramiding of resistance loci for effective control of FHB.
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http://dx.doi.org/10.1007/s00122-015-2485-1DOI Listing
June 2015

Cloning and characterization of a critical regulator for preharvest sprouting in wheat.

Genetics 2013 Sep 2;195(1):263-73. Epub 2013 Jul 2.

Department of Agronomy, Kansas State University, Manhattan, Kansas 66506.

Sprouting of grains in mature spikes before harvest is a major problem in wheat (Triticum aestivum) production worldwide. We cloned and characterized a gene underlying a wheat quantitative trait locus (QTL) on the short arm of chromosome 3A for preharvest sprouting (PHS) resistance in white wheat using comparative mapping and map-based cloning. This gene, designated TaPHS1, is a wheat homolog of a MOTHER OF FLOWERING TIME (TaMFT)-like gene. RNA interference-mediated knockdown of the gene confirmed that TaPHS1 positively regulates PHS resistance. We discovered two causal mutations in TaPHS1 that jointly altered PHS resistance in wheat. One GT-to-AT mutation generates a mis-splicing site, and the other A-to-T mutation creates a premature stop codon that results in a truncated nonfunctional transcript. Association analysis of a set of wheat cultivars validated the role of the two mutations on PHS resistance. The molecular characterization of TaPHS1 is significant for expediting breeding for PHS resistance to protect grain yield and quality in wheat production.
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http://dx.doi.org/10.1534/genetics.113.152330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3761307PMC
September 2013

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.

Proc Natl Acad Sci U S A 2013 May 22;110(19):7940-5. Epub 2013 Apr 22.

Department of Plant Sciences, University of California, Davis, CA 95616, USA.

The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii, the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.
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http://dx.doi.org/10.1073/pnas.1219082110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651469PMC
May 2013

A diploid wheat TILLING resource for wheat functional genomics.

BMC Plant Biol 2012 Nov 7;12:205. Epub 2012 Nov 7.

Wheat Genetic and Genomic Resources Center, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA.

Background: Triticum monococcum L., an A genome diploid einkorn wheat, was the first domesticated crop. As a diploid, it is attractive genetic model for the study of gene structure and function of wheat-specific traits. Diploid wheat is currently not amenable to reverse genetics approaches such as insertion mutagenesis and post-transcriptional gene silencing strategies. However, TILLING offers a powerful functional genetics approach for wheat gene analysis.

Results: We developed a TILLING population of 1,532 M2 families using EMS as a mutagen. A total of 67 mutants were obtained for the four genes studied. Waxy gene mutation frequencies are known to be 1/17.6 - 34.4 kb DNA in polyploid wheat TILLING populations. The T. monococcum diploid wheat TILLING population had a mutation frequency of 1/90 kb for the same gene. Lignin biosynthesis pathway genes- COMT1, HCT2, and 4CL1 had mutation frequencies of 1/86 kb, 1/92 kb and 1/100 kb, respectively. The overall mutation frequency of the diploid wheat TILLING population was 1/92 kb.

Conclusion: The mutation frequency of a diploid wheat TILLING population was found to be higher than that reported for other diploid grasses. The rate, however, is lower than tetraploid and hexaploid wheat TILLING populations because of the higher tolerance of polyploids to mutations. Unlike polyploid wheat, most mutants in diploid wheat have a phenotype amenable to forward and reverse genetic analysis and establish diploid wheat as an attractive model to study gene function in wheat. We estimate that a TILLING population of 5, 520 will be needed to get a non-sense mutation for every wheat gene of interest with 95% probability.
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http://dx.doi.org/10.1186/1471-2229-12-205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541219PMC
November 2012

Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat.

BMC Plant Biol 2012 May 4;12:64. Epub 2012 May 4.

Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.

Background: Bread wheat, one of the world's staple food crops, has the largest, highly repetitive and polyploid genome among the cereal crops. The wheat genome holds the key to crop genetic improvement against challenges such as climate change, environmental degradation, and water scarcity. To unravel the complex wheat genome, the International Wheat Genome Sequencing Consortium (IWGSC) is pursuing a chromosome- and chromosome arm-based approach to physical mapping and sequencing. Here we report on the use of a BAC library made from flow-sorted telosomic chromosome 3A short arm (t3AS) for marker development and analysis of sequence composition and comparative evolution of homoeologous genomes of hexaploid wheat.

Results: The end-sequencing of 9,984 random BACs from a chromosome arm 3AS-specific library (TaaCsp3AShA) generated 11,014,359 bp of high quality sequence from 17,591 BAC-ends with an average length of 626 bp. The sequence represents 3.2% of t3AS with an average DNA sequence read every 19 kb. Overall, 79% of the sequence consisted of repetitive elements, 1.38% as coding regions (estimated 2,850 genes) and another 19% of unknown origin. Comparative sequence analysis suggested that 70-77% of the genes present in both 3A and 3B were syntenic with model species. Among the transposable elements, gypsy/sabrina (12.4%) was the most abundant repeat and was significantly more frequent in 3A compared to homoeologous chromosome 3B. Twenty novel repetitive sequences were also identified using de novo repeat identification. BESs were screened to identify simple sequence repeats (SSR) and transposable element junctions. A total of 1,057 SSRs were identified with a density of one per 10.4 kb, and 7,928 junctions between transposable elements (TE) and other sequences were identified with a density of one per 1.39 kb. With the objective of enhancing the marker density of chromosome 3AS, oligonucleotide primers were successfully designed from 758 SSRs and 695 Insertion Site Based Polymorphisms (ISBPs). Of the 96 ISBP primer pairs tested, 28 (29%) were 3A-specific and compared to 17 (18%) for 96 SSRs.

Conclusion: This work reports on the use of wheat chromosome arm 3AS-specific BAC library for the targeted generation of sequence data from a particular region of the huge genome of wheat. A large quantity of sequences were generated from the A genome of hexaploid wheat for comparative genome analysis with homoeologous B and D genomes and other model grass genomes. Hundreds of molecular markers were developed from the 3AS arm-specific sequences; these and other sequences will be useful in gene discovery and physical mapping.
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http://dx.doi.org/10.1186/1471-2229-12-64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438119PMC
May 2012

Characterization of the genome of bald cypress.

BMC Genomics 2011 Nov 11;12:553. Epub 2011 Nov 11.

Mississippi Genome Exploration Laboratory and Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA.

Background: Bald cypress (Taxodium distichum var. distichum) is a coniferous tree of tremendous ecological and economic importance. It is a member of the family Cupressaceae which also includes cypresses, redwoods, sequoias, thujas, and junipers. While the bald cypress genome is more than three times the size of the human genome, its 1C DNA content is amongst the smallest of any conifer. To learn more about the genome of bald cypress and gain insight into the evolution of Cupressaceae genomes, we performed a Cot analysis and used Cot filtration to study Taxodium DNA. Additionally, we constructed a 6.7 genome-equivalent BAC library that we screened with known Taxodium genes and select repeats.

Results: The bald cypress genome is composed of 90% repetitive DNA with most sequences being found in low to mid copy numbers. The most abundant repeats are found in fewer than 25,000 copies per genome. Approximately 7.4% of the genome is single/low-copy DNA (i.e., sequences found in 1 to 5 copies). Sequencing of highly repetitive Cot clones indicates that most Taxodium repeats are highly diverged from previously characterized plant repeat sequences. The bald cypress BAC library consists of 606,336 clones (average insert size of 113 kb) and collectively provides 6.7-fold genome equivalent coverage of the bald cypress genome. Macroarray screening with known genes produced, on average, about 1.5 positive clones per probe per genome-equivalent. Library screening with Cot-1 DNA revealed that approximately 83% of BAC clones contain repetitive sequences iterated 103 to 104 times per genome.

Conclusions: The BAC library for bald cypress is the first to be generated for a conifer species outside of the family Pinaceae. The Taxodium BAC library was shown to be useful in gene isolation and genome characterization and should be an important tool in gymnosperm comparative genomics, physical mapping, genome sequencing, and gene/polymorphism discovery. The single/low-copy (SL) component of bald cypress is 4.6 times the size of the Arabidopsis genome. As suggested for other gymnosperms, the large amount of SL DNA in Taxodium is likely the result of divergence among ancient repeat copies and gene/pseudogene duplication.
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http://dx.doi.org/10.1186/1471-2164-12-553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228858PMC
November 2011

Molecular mapping of QTLs for Karnal bunt resistance in two recombinant inbred populations of bread wheat.

Theor Appl Genet 2007 Dec 19;116(1):147-54. Epub 2007 Oct 19.

Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.

Karnal bunt (KB) of wheat, caused by the fungus Tilletia indica, is a challenge to the grain industry, owing not to direct yield loss but to quarantine regulations that may restrict international movement of affected grain. Several different sources of resistance to KB have been reported. Understanding the genetics of resistance will facilitate the introgression of resistance into new wheat cultivars. The objectives of this study were to identify quantitative trait loci (QTLs) associated with KB resistance and to identify DNA markers in two recombinant inbred line populations derived from crosses of the susceptible cultivar WH542 with resistant lines HD29 and W485. Populations were evaluated for resistance against the KB pathogen for 3 years at Punjab Agricultural University, Ludhiana, India. Two new QTLs (Qkb.ksu-5BL.1 and Qkb.ksu-6BS.1) with resistance alleles from HD29 were identified and mapped in the intervals Xgdm116-Xwmc235 on chromosome 5B (deletion bin 5BL9-0.76-0.79) and Xwmc105-Xgwm88 on chromosome 6B (C-6BS5-0.76). They explained up to 19 and 13% of phenotypic variance, respectively. Another QTL (Qkb.ksu-4BL.1) with a resistance allele from W485 mapped in the interval Xgwm6-Xwmc349 on chromosome 4B (4BL5-0.86-1.00) and explained up to 15% of phenotypic variance. Qkb.ksu-6BS.1 showed pairwise interactions with loci on chromosomes 3B and 6A. Markers suitable for marker-assisted selection are available for all three QTLs.
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http://dx.doi.org/10.1007/s00122-007-0654-6DOI Listing
December 2007
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