Publications by authors named "Velu Govindan"

23 Publications

  • Page 1 of 1

Target Population of Environments for Wheat Breeding in India: Definition, Prediction and Genetic Gains.

Front Plant Sci 2021 24;12:638520. Epub 2021 May 24.

Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.

In this study, we defined the target population of environments (TPE) for wheat breeding in India, the largest wheat producer in South Asia, and estimated the correlated response to the selection and prediction ability of five selection environments (SEs) in Mexico. We also estimated grain yield (GY) gains in each TPE. Our analysis used meteorological, soil, and GY data from the international Elite Spring Wheat Yield Trials (ESWYT) distributed by the International Maize and Wheat Improvement Center (CIMMYT) from 2001 to 2016. We identified three TPEs: TPE 1, the optimally irrigated Northwestern Plain Zone; TPE 2, the optimally irrigated, heat-stressed North Eastern Plains Zone; and TPE 3, the drought-stressed Central-Peninsular Zone. The correlated response to selection ranged from 0.4 to 0.9 within each TPE. The highest prediction accuracies for GY per TPE were derived using models that included genotype-by-environment interaction and/or meteorological information and their interaction with the lines. The highest prediction accuracies for TPEs 1, 2, and 3 were 0.37, 0.46, and 0.51, respectively, and the respective GY gains were 118, 46, and 123 kg/ha/year. These results can help fine-tune the breeding of elite wheat germplasm with stable yields to reduce farmers' risk from year-to-year environmental variation in India's wheat lands, which cover 30 million ha, account for 100 million tons of grain or more each year, and provide food and livelihoods for hundreds of millions of farmers and consumers in South Asia.
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http://dx.doi.org/10.3389/fpls.2021.638520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8181127PMC
May 2021

Elucidating the genetics of grain yield and stress-resilience in bread wheat using a large-scale genome-wide association mapping study with 55,568 lines.

Sci Rep 2021 Mar 4;11(1):5254. Epub 2021 Mar 4.

International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.

Wheat grain yield (GY) improvement using genomic tools is important for achieving yield breakthroughs. To dissect the genetic architecture of wheat GY potential and stress-resilience, we have designed this large-scale genome-wide association study using 100 datasets, comprising 105,000 GY observations from 55,568 wheat lines evaluated between 2003 and 2019 by the International Maize and Wheat Improvement Center and national partners. We report 801 GY-associated genotyping-by-sequencing markers significant in more than one dataset and the highest number of them were on chromosomes 2A, 6B, 6A, 5B, 1B and 7B. We then used the linkage disequilibrium (LD) between the consistently significant markers to designate 214 GY-associated LD-blocks and observed that 84.5% of the 58 GY-associated LD-blocks in severe-drought, 100% of the 48 GY-associated LD-blocks in early-heat and 85.9% of the 71 GY-associated LD-blocks in late-heat, overlapped with the GY-associated LD-blocks in the irrigated-bed planting environment, substantiating that simultaneous improvement for GY potential and stress-resilience is feasible. Furthermore, we generated the GY-associated marker profiles and analyzed the GY favorable allele frequencies for a large panel of 73,142 wheat lines, resulting in 44.5 million datapoints. Overall, the extensive resources presented in this study provide great opportunities to accelerate breeding for high-yielding and stress-resilient wheat varieties.
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http://dx.doi.org/10.1038/s41598-021-84308-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7933281PMC
March 2021

Haplotype-Based, Genome-Wide Association Study Reveals Stable Genomic Regions for Grain Yield in CIMMYT Spring Bread Wheat.

Front Genet 2020 3;11:589490. Epub 2020 Dec 3.

International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.

We untangled key regions of the genetic architecture of grain yield (GY) in CIMMYT spring bread wheat by conducting a haplotype-based, genome-wide association study (GWAS), together with an investigation of epistatic interactions using seven large sets of elite yield trials (EYTs) consisting of a total of 6,461 advanced breeding lines. These lines were phenotyped under irrigated and stress environments in seven growing seasons (2011-2018) and genotyped with genotyping-by-sequencing markers. Genome-wide 519 haplotype blocks were constructed, using a linkage disequilibrium-based approach covering 14,036 Mb in the wheat genome. Haplotype-based GWAS identified 7, 4, 10, and 15 stable (significant in three or more EYTs) associations in irrigated (I), mild drought (MD), severe drought (SD), and heat stress (HS) testing environments, respectively. Considering all EYTs and the four testing environments together, 30 stable associations were deciphered with seven hotspots identified on chromosomes 1A, 1B, 2B, 4A, 5B, 6B, and 7B, where multiple haplotype blocks were associated with GY. Epistatic interactions contributed significantly to the genetic architecture of GY, explaining variation of 3.5-21.1%, 3.7-14.7%, 3.5-20.6%, and 4.4- 23.1% in I, MD, SD, and HS environments, respectively. Our results revealed the intricate genetic architecture of GY, controlled by both main and epistatic effects. The importance of these results for practical applications in the CIMMYT breeding program is discussed.
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http://dx.doi.org/10.3389/fgene.2020.589490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7737720PMC
December 2020

Genomic Selection for Grain Yield in the CIMMYT Wheat Breeding Program-Status and Perspectives.

Front Plant Sci 2020 15;11:564183. Epub 2020 Sep 15.

Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States.

Genomic breeding technologies offer new opportunities for grain yield (GY) improvement in common wheat. In this study, we have evaluated the potential of genomic selection (GS) in breeding for GY in wheat by modeling a large dataset of 48,562 GY observations from the International Maize and Wheat Improvement Center (CIMMYT), including 36 yield trials evaluated between 2012 and 2019 in Obregón, Sonora, Mexico. Our key objective was to determine the value that GS can add to the current three-stage yield testing strategy at CIMMYT, and we draw inferences from predictive modeling of GY using 420 different populations, environments, cycles, and model combinations. First, we evaluated the potential of genomic predictions for minimizing the number of replications and lines tested within a site and year and obtained mean prediction accuracies (PAs) of 0.56, 0.5, and 0.42 in Stages 1, 2, and 3 of yield testing, respectively. However, these PAs were similar to the mean pedigree-based PAs indicating that genomic relationships added no value to pedigree relationships in the yield testing stages, characterized by small family-sizes. Second, we evaluated genomic predictions for minimizing GY testing across stages/years in Obregón and observed mean PAs of 0.41, 0.31, and 0.37, respectively when GY in the full irrigation bed planting (FI BP), drought stress (DS), and late-sown heat stress environments were predicted across years using genotype × environment (G × E) interaction models. Third, we evaluated genomic predictions for minimizing the number of yield testing environments and observed that in Stage 2, the FI BP, full irrigation flat planting and early-sown heat stress environments (mean PA of 0.37 ± 0.12) and the reduced irrigation and DS environments (mean PA of 0.45 ± 0.07) had moderate predictabilities among them. However, in both predictions across years and environments, the PAs were inconsistent across years and the G × E models had no advantage over the baseline model with environment and line effects. Overall, our results provide excellent insights into the predictability of a quantitative trait like GY and will have important implications on the future design of GS for GY in wheat breeding programs globally.
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http://dx.doi.org/10.3389/fpls.2020.564183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522222PMC
September 2020

Grain yield genetic gains and changes in physiological related traits for CIMMYT's High Rainfall Wheat Screening Nursery tested across international environments.

Field Crops Res 2020 Apr;249:107742

Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Global Wheat Program, Apdo. 0660, Mexico City, Mexico.

The effects of climate change together with the projected future demand represents a huge challenge for wheat production systems worldwide. Wheat breeding can contribute to global food security through the creation of genotypes exhibiting stress tolerance and higher yield potential. The objectives of our study were to () estimate the annual grain yield (GY) genetic gain of High Rainfall Wheat Yield Trials (HRWYT) grown from 2007 (15th HRWYT) to 2016 (24th HRWYT) across international environments, and () determine the changes in physiological traits associated with GY genetic improvement. The GY genetic gains were estimated as genetic progress (GYP) and in terms of local checks (GYLC). In total, 239 international locations were classified into two groups: high- and low-rainfall environments based on climate variables and trial management practices. In the high-rainfall environment, the annual genetic gains for GYP and GYLC were 3.8 and 1.17 % (160 and 65.1 kg ha yr), respectively. In the low-rainfall environment, the genetic gains were 0.93 and 0.73 % (40 and 33.1 kg ha yr), for GYP and GYLC respectively. The GY of the lines included in each nursery showed a significant phenotypic correlation between high- and low-rainfall environments in all the examined years and several of the five best performing lines were common in both environments. The GY progress was mainly associated with increased grain weight (R = 0.35 < 0.001), days to maturity (R = 0.20, < 0.001) and grain filling period (R = 0.06, < 0.05). These results indicate continuous GY genetic progress and yield stability in the HRWYT germplasm developed and distributed by CIMMYT.
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http://dx.doi.org/10.1016/j.fcr.2020.107742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079639PMC
April 2020

Genetic dissection of zinc, iron, copper, manganese and phosphorus in wheat (Triticum aestivum L.) grain and rachis at two developmental stages.

Plant Sci 2020 Feb 11;291:110338. Epub 2019 Dec 11.

College of Science and Engineering, Flinders University, SA 5042, Australia.

The development of high-yielding wheat genotypes containing micronutrient-dense grains are the main priorities of biofortification programs. At the International Maize and Wheat Improvement Center, breeders have successfully crossed high zinc progenitors including synthetic hexaploid wheat, T. dicoccum, T. spelta and landraces to generate high-zinc varieties. In this study, we report a genome-wide association using a wheat diversity panel to dissect the genetics controlling zinc, iron, copper, manganese and phosphorus concentrations in the grain and rachis during grain development and at physiological maturity. Significant marker-trait associations (MTAs) were identified for each nutrient using multi-locus mixed model methodologies. For mature grain, markers that showed significant pleiotropic effects were found on chromosomes 1A, 3B and 5B, of which those on chromosome 5B at ∼95.5 cM were consistent over two growing seasons. Co-located MTAs were identified for the nutrient concentrations in developing grain, rachis and mature grain on multiple chromosomes. The identified genomic regions included putative candidate genes involved in metal uptake and transport and storage protein processing. These findings add to our understanding of the genetics of the five important nutrients in wheat grain and provide information on genetic markers for selecting high micronutrient genotypes.
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http://dx.doi.org/10.1016/j.plantsci.2019.110338DOI Listing
February 2020

Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics.

Nat Genet 2019 10 23;51(10):1530-1539. Epub 2019 Sep 23.

International Maize And Wheat Improvement Center (CIMMYT), Texcoco, Mexico.

Bread wheat improvement using genomic tools is essential for accelerating trait genetic gains. Here we report the genomic predictabilities of 35 key traits and demonstrate the potential of genomic selection for wheat end-use quality. We also performed a large genome-wide association study that identified several significant marker-trait associations for 50 traits evaluated in South Asia, Africa and the Americas. Furthermore, we built a reference wheat genotype-phenotype map, explored allele frequency dynamics over time and fingerprinted 44,624 wheat lines for trait-associated markers, generating over 7.6 million data points, which together will provide a valuable resource to the wheat community for enhancing productivity and stress resilience.
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http://dx.doi.org/10.1038/s41588-019-0496-6DOI Listing
October 2019

Economic benefits of blast-resistant biofortified wheat in Bangladesh: The case of .

Crop Prot 2019 Sep;123:45-58

Socioeconomics Program, CIMMYT, Mexico.

The first occurrence of wheat blast in 2016 threatened Bangladesh's already precarious food security situation. The Bangladesh Agricultural Research Institute (BARI), together with the International Maize and Wheat Improvement Center (CIMMYT) developed and released the wheat variety 33 that is resistant to wheat blast and other common diseases. The new variety provides a 5-8% yield gain over the available popular varieties, as well as being zinc enriched. This study examines the potential economic benefits of in Bangladesh. First, applying a climate analogue model, this study identified that more than 55% of the total wheat-growing area in Bangladesh (across 45 districts) is vulnerable to wheat blast. Second, applying an impact assessment framework, this study shows that with an assumed cumulative adoption starting from 2019-20 and increasing to 30% by 2027-28, the potential economic benefits of the newly developed wheat variety far exceeds its dissemination cost by 2029-30. Even if dissemination of the new wheat variety is limited to only the ten currently blast-affected districts, the yearly average net benefits could amount to USD 0.23-1.6 million. Based on the findings, international funder agencies are urged to support the national system in scaling out the new wheat variety and wheat research in general to ensure overall food security in Bangladesh and South Asia.
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http://dx.doi.org/10.1016/j.cropro.2019.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686726PMC
September 2019

QTL mapping for micronutrients concentration and yield component traits in a hexaploid wheat mapping population.

J Cereal Sci 2019 Jul;88:57-64

International Maize and Wheat Improvement Center (CIMMYT), Apdo Postal 6-641, Mexico DF, 06600, Mexico.

Bread wheat is a major staple cereal provides more than 20% of dietary energy and protein supply to global population. However, with increasing population growth, the problem of nutritional deficiencies is increasingly affecting the health of resource people with predominantly cereal-based diet. Therefore, the development of wheat genotypes with micronutrient-dense grains along with high-yield potential is one of the major priorities of wheat biofortification program at CIMMYT. We conducted a QTL mapping study using a recombinant inbred line (RIL) population derived from a cross between a Chinese parental line with highGZnC and a Mexican commercial bread wheat cultivar Roelfs F2007 to identify QTLs that could potentially be integrated in mineral nutrient concentrations and agronomic-related traits breeding. We evaluated 200 RIL lines for mineral nutrient concentrations and agronomic-related traits over two years. A total of 60 QTLs were detected, of which 10 QTLs for GZnC, 9 for GFeC, 5 for GPC and 36 for agronomic-related traits. Moreover, a total of 55 promising candidate genes were identified from the list of associated markers for GFeC and GZnC using the recently annotated wheat genome sequence. We identified the promising genomic regions with high mineral nutrient concentrations and acceptable yield potential, which are good resource for further use in wheat biofortification breeding programs.
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http://dx.doi.org/10.1016/j.jcs.2019.05.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7729826PMC
July 2019

High-throughput phenotyping platforms enhance genomic selection for wheat grain yield across populations and cycles in early stage.

Theor Appl Genet 2019 Jun 18;132(6):1705-1720. Epub 2019 Feb 18.

Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.

Genomic selection (GS) models have been validated for many quantitative traits in wheat (Triticum aestivum L.) breeding. However, those models are mostly constrained within the same growing cycle and the extension of GS to the case of across cycles has been a challenge, mainly due to the low predictive accuracy resulting from two factors: reduced genetic relationships between different families and augmented environmental variances between cycles. Using the data collected from diverse field conditions at the International Wheat and Maize Improvement Center, we evaluated GS for grain yield in three elite yield trials across three wheat growing cycles. The objective of this project was to employ the secondary traits, canopy temperature, and green normalized difference vegetation index, which are closely associated with grain yield from high-throughput phenotyping platforms, to improve prediction accuracy for grain yield. The ability to predict grain yield was evaluated reciprocally across three cycles with or without secondary traits. Our results indicate that prediction accuracy increased by an average of 146% for grain yield across cycles with secondary traits. In addition, our results suggest that secondary traits phenotyped during wheat heading and early grain filling stages were optimal for enhancing the prediction accuracy for grain yield.
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http://dx.doi.org/10.1007/s00122-019-03309-0DOI Listing
June 2019

Assessing Genetic Diversity to Breed Competitive Biofortified Wheat With Enhanced Grain Zn and Fe Concentrations.

Front Plant Sci 2018 10;9:1971. Epub 2019 Jan 10.

Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.

Breeding wheat with enhanced levels of grain zinc (Zn) and iron (Fe) is a cost-effective, sustainable solution to malnutrition problems. Modern wheat varieties have limited variation in grain Zn and Fe, but large-scale screening has identified high levels of Zn and Fe in wild relatives and progenitors of cultivated wheat. The most promising sources of high Zn and Fe are einkorn (), wild emmer (), diploid progenitors of hexaploid wheat (such as , and landraces of . This study evaluate the effects of translocations from rye and different species in a "Pavon-76" wheat genetic background and utilized in the wheat biofortification breeding program at CIMMYT that uses diverse genetic resources, including landraces, recreated synthetic hexaploids, and pre-breeding lines. Four translocations were identified that resulted significantly higher Zn content in "Pavon 76" genetic background than the check varieties, and they had increased levels of grain Fe as well-compared to "Pavon 76." These lines were also included in the breeding program aimed to develop advanced high Zn breeding lines. Advanced lines derived from diverse crosses were screened under Zn-enriched soil conditions in Mexico during the 2017 and 2018 seasons. The Zn content of the grain was ranging from 35 to 69 mg/kg during 2017 and 38 to 72 mg/kg during 2018. Meanwhile grain Fe ranged from 30 to 43 mg/kg during 2017 and 32 to 52 mg/kg during 2018. A highly significant positive correlation was found between Zn and Fe ( = 0.54; < 0.001) content of the breeding lines, therefore it was possible to breed for both properties in parallel. Yield testing of the advanced lines showed that 15% (2017) and 24% (2018) of the lines achieved 95-110% yield potential of the commercial checks and also had 12 mg/kg advantage in the Zn content suggesting that greater genetic gains and farmer-preferred wheat varieties were developed and deployed. A decade of research and breeding efforts led to the selection of "best-bet" breeding lines and the release of eight biofortified wheat varieties in target regions of South Asia and in Mexico.
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http://dx.doi.org/10.3389/fpls.2018.01971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335970PMC
January 2019

Prospects and Challenges of Applied Genomic Selection-A New Paradigm in Breeding for Grain Yield in Bread Wheat.

Plant Genome 2018 11;11(3)

Genomic selection (GS) has been promising for increasing genetic gains in several species. Therefore, we evaluated the potential integration of GS for grain yield (GY) in bread wheat ( L.) in CIMMYT's elite yield trial nurseries. We observed that the genomic prediction accuracies within nurseries (0.44 and 0.35) were substantially higher than across-nursery accuracies (0.15 and 0.05) for GY evaluated in the bed and flat planting systems, respectively. The accuracies from using only a subset of 251 genotyping-by-sequencing markers were comparable to the accuracies using all 2038 markers. We also used the item-based collaborative filtering approach for incorporating other related traits in predicting GY and observed that it outperformed genomic predictions across nurseries, but was less predictive when trait correlations with GY were low. Furthermore, we compared GS and phenotypic selections (PS) and observed that at a selection intensity of 0.5, GS could select a maximum of 70.9 and 61.5% of the top lines and discard 71.5 and 60.5% of the poor lines selected or discarded by PS within and across nurseries, respectively. Comparisons of GS and pedigree-based predictions revealed that the advantage of GS over the pedigree was moderate in populations without full-sibs. However, GS was less advantageous for within-family selections in elite families with few full-sibs and minimal Mendelian sampling variance. Overall, our results demonstrate the importance of applying GS for GY at the appropriate stage of the breeding cycle, and we speculate that gains can be maximized if it is implemented in early-generation within-family selections.
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http://dx.doi.org/10.3835/plantgenome2018.03.0017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7822054PMC
November 2018

Integrating genomic-enabled prediction and high-throughput phenotyping in breeding for climate-resilient bread wheat.

Theor Appl Genet 2019 Jan 19;132(1):177-194. Epub 2018 Oct 19.

International Maize and Wheat Improvement Center (CIMMYT), Postal 6-641, 06600, Mexico, D.F., Mexico.

Genomic selection and high-throughput phenotyping (HTP) are promising tools to accelerate breeding gains for high-yielding and climate-resilient wheat varieties. Hence, our objective was to evaluate them for predicting grain yield (GY) in drought-stressed (DS) and late-sown heat-stressed (HS) environments of the International maize and wheat improvement center's elite yield trial nurseries. We observed that the average genomic prediction accuracies using fivefold cross-validations were 0.50 and 0.51 in the DS and HS environments, respectively. However, when a different nursery/year was used to predict another nursery/year, the average genomic prediction accuracies in the DS and HS environments decreased to 0.18 and 0.23, respectively. While genomic predictions clearly outperformed pedigree-based predictions across nurseries, they were similar to pedigree-based predictions within nurseries due to small family sizes. In populations with some full-sibs in the training population, the genomic and pedigree-based prediction accuracies were on average 0.27 and 0.35 higher than the accuracies in populations with only one progeny per cross, indicating the importance of genetic relatedness between the training and validation populations for good predictions. We also evaluated the item-based collaborative filtering approach for multivariate prediction of GY using the green normalized difference vegetation index from HTP. This approach proved to be the best strategy for across-nursery predictions, with average accuracies of 0.56 and 0.62 in the DS and HS environments, respectively. We conclude that GY is a challenging trait for across-year predictions, but GS and HTP can be integrated in increasing the size of populations screened and evaluating unphenotyped large nurseries for stress-resilience within years.
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http://dx.doi.org/10.1007/s00122-018-3206-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320358PMC
January 2019

Genetic dissection of grain zinc concentration in spring wheat for mainstreaming biofortification in CIMMYT wheat breeding.

Sci Rep 2018 09 10;8(1):13526. Epub 2018 Sep 10.

CIMMYT, Global Wheat Program, New Delhi, India.

Wheat is an important staple that acts as a primary source of dietary energy, protein, and essential micronutrients such as iron (Fe) and zinc (Zn) for the world's population. Approximately two billion people suffer from micronutrient deficiency, thus breeders have crossed high Zn progenitors such as synthetic hexaploid wheat, T. dicoccum, T. spelta, and landraces to generate wheat varieties with competitive yield and enhanced grain Zn that are being adopted by farmers in South Asia. Here we report a genome-wide association study (GWAS) using the wheat Illumina iSelect 90 K Infinitum SNP array to characterize grain Zn concentrations in 330 bread wheat lines. Grain Zn phenotype of this HarvestPlus Association Mapping (HPAM) panel was evaluated across a range of environments in India and Mexico. GWAS analysis revealed 39 marker-trait associations for grain Zn. Two larger effect QTL regions were found on chromosomes 2 and 7. Candidate genes (among them zinc finger motif of transcription-factors and metal-ion binding genes) were associated with the QTL. The linked markers and associated candidate genes identified in this study are being validated in new biparental mapping populations for marker-assisted breeding.
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http://dx.doi.org/10.1038/s41598-018-31951-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6131222PMC
September 2018

Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security.

Sci Rep 2018 08 21;8(1):12527. Epub 2018 Aug 21.

ICAR-Indian Agricultural Research Institute, Regional Station, Shimla, 171004, India.

The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the 'T' allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT's best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios.
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http://dx.doi.org/10.1038/s41598-018-30667-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104032PMC
August 2018

Genetic impact of dwarfing genes on grain micronutrients concentration in wheat.

Field Crops Res 2017 Dec;214:373-377

Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo Postal 6-641, Mexico DF, Mexico.

Wheat is a major staple food crop providing about 20% of dietary energy and proteins, and food products made of whole grain wheat are a major source of micronutrients like Zinc (Zn), Iron (Fe), Manganese (Mn), Magnesium (Mg), Vitamin B and E. Wheat provides about 40% intake of essential micronutrients by humans in the developing countries relying on wheat based diets. Varieties with genetically enhanced levels of grain micronutrient concentrations can provide a cost-effective and sustainable option to resource poor wheat consumers. To determine the effects of commonly deployed dwarfing genes on wheat grain Zn, Fe, Mn and Mg concentrations, nine bread wheat () and six durum wheat () isoline pairs differing for (= ) and one bread wheat pair for (= ) dwarfing genes were evaluated for three crop seasons at N.E. Borlaug Research Station, Cd. Obregon, Sonora, Mexico. Presence of dwarfing genes have significantly reduced grain Zn concentration by 3.9 ppm (range 1.9-10.0 ppm), and Fe by 3.2 ppm (range 1.0-14.4 ppm). On the average, about 94 ppm Mg and 6 ppm Mn reductions occurred in semidwarf varieties compared to tall varieties. The thousand kernel weight (TKW) of semidwarf isolines was 2.6 g (range 0.7-5.6 g) lower than the tall counterparts whereas the plant height decreased by 25 cm (range 16-37 cm). Reductions for all traits in semidwarfs were genotype dependent and the magnitude of height reductions did not correlate with reductions in micronutrient concentrations in wheat grain. We conclude that increased grain yield potential of semidwarf wheat varieties is associated with reduced grain micronutrient concentrations; however, the magnitude of reductions in micronutrients varied depending on genetic background and their associated pleiotropic effect on yield components.
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http://dx.doi.org/10.1016/j.fcr.2017.09.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5669307PMC
December 2017

QTL Mapping of Grain Zn and Fe Concentrations in Two Hexaploid Wheat RIL Populations with Ample Transgressive Segregation.

Front Plant Sci 2017 18;8:1800. Epub 2017 Oct 18.

Global Wheat Program, Centro Internacional de Mejoramiento de Maíz y Trigo, Texcoco, Mexico.

More than 50% of undernourished children live in Asia and more than 25% live in Africa. Coupled with an inadequate food supply, mineral deficiencies are widespread in these populations; particularly zinc (Zn) and iron (Fe) deficiencies that lead to retarded growth, adverse effects on both the immune system and an individual's cognitive abilities. Biofortification is one solution aimed at reducing the incidence of these deficiencies. To efficiently breed a biofortified wheat variety, it is important to generate knowledge of the genomic regions associated with grain Zn (GZn) and Fe (GFe) concentration. This allows for the introgression of favorable alleles into elite germplasm. In this study we evaluated two bi-parental populations of 188 recombinant inbred lines (RILs) displaying a significant range of transgressive segregation for GZn and GFe during three crop cycles in CIMMYT, Mexico. Parents of the RILs were derived from L. and synthetic hexaploid wheat crosses. QTL analysis identified a number of significant QTL with a region denominated as on chromosome 7B explaining the largest (32.7%) proportion of phenotypic variance (PVE) for GZn and leading to an average additive effect of -1.3. The QTL with the largest average additive effect for GFe (-0.161) was found on chromosome 4A (), with 21.14% of the PVE. The region co-localized closest to the region in a consensus map built from the linkage maps of both populations. Pleiotropic or tightly linked QTL were also found on chromosome 3B, however of minor effects and PVE between 4.3 and 10.9%. Further efforts are required to utilize the QTL information in marker assisted backcrossing schemes for wheat biofortification. A strategy to follow is to intercross the transgressive individuals from both populations and then utilize them as sources in biofortification breeding pipelines.
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http://dx.doi.org/10.3389/fpls.2017.01800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5651365PMC
October 2017

Variability in iron, zinc and phytic acid content in a worldwide collection of commercial durum wheat cultivars and the effect of reduced irrigation on these traits.

Food Chem 2017 Dec 22;237:499-505. Epub 2017 May 22.

Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico DF, Mexico. Electronic address:

Diets very rich in cereals have been associated with micronutrient malnutrition, and the biofortification of them, has been proposed as one of the best approaches to alleviate the problem. Durum wheat is one of the main sources of calories and protein in many developing countries. In this study, 46 durum varieties grown under full and reduced irrigation, were analyzed for micronutrients and phytate content to determine the potential bioavailability of the micronutrients. The variation was 25.7-40.5mg/kg for iron and of 24.8-48.8mg/kg for zinc. For phytate determination (0.462-0.952 %), a modified methodology was validated in order to reduce testing costs while speeding up testing time. Variation was detected for phytate:iron and zinc molar ratios (12.1-29.6 and 16.9-23.6, respectively). The results could be useful to generate varieties with appropriate levels of phytate and micronutrients, which can lead to the development of varieties rich in micronutrients to overcome malnutrition.
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http://dx.doi.org/10.1016/j.foodchem.2017.05.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544597PMC
December 2017

Genetic Yield Gains In CIMMYT's International Elite Spring Wheat Yield Trials By Modeling The Genotype × Environment Interaction.

Crop Sci 2017 Mar-Apr;57:789-801. Epub 2017 Jan 12.

CIMMYT, Global Wheat Program, Apdo. 0660, Mexico City, México.

We calculated the annual genetic gains for grain yield (GY) of wheat ( L.) achieved over 8 yr of international Elite Spring Wheat Yield Trials (ESWYT), from 2006-2007 (27th ESWYT) to 2014-2015 (34th ESWYT). In total, 426 locations were classified within three main megaenvironments (MEs): ME1 (optimally irrigated environments), ME4 (drought-stressed environments), and ME5 (heat-stressed environments). By fitting a factor analytical structure for modeling the genotype environment (G E) interaction, we measured GY gains relative to the widely grown cultivar Attila (GYA) and to the local checks (GYLC). Genetic gains for GYA and GYLC across locations were 1.67 and 0.53% (90.1 and 28.7 kg ha yr), respectively. In ME1, genetic gains were 1.63 and 0.72% (102.7 and 46.65 kg ha yr) for GYA and GYLC, respectively. In ME4, genetic gains were 2.7 and 0.41% (88 and 15.45 kg ha yr) for GYA and GYLC, respectively. In ME5, genetic gains were 0.31 and 1.0% (11.28 and 36.6 kg ha yr) for GYA and GYLC, respectively. The high GYA in ME1 and ME4 can be partially attributed to yellow rust races that affect Attila. When G E interactions were not modeled, genetic gains were lower. Analyses showed that CIMMYT's location at Ciudad Obregon, Mexico, is highly correlated with locations in other countries in ME1. Lines that were top performers in more than one ME and more than one country were identified. CIMMYT's breeding program continues to deliver improved and widely adapted germplasm for target environments.
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http://dx.doi.org/10.2135/cropsci2016.06.0553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7680939PMC
January 2017

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches.

Front Plant Sci 2016 6;7:991. Epub 2016 Jul 6.

International Maize and Wheat Improvement Center Texcoco, Mexico.

Current trends in population growth and consumption patterns continue to increase the demand for wheat, a key cereal for global food security. Further, multiple abiotic challenges due to climate change and evolving pathogen and pests pose a major concern for increasing wheat production globally. Triticeae species comprising of primary, secondary, and tertiary gene pools represent a rich source of genetic diversity in wheat. The conventional breeding strategies of direct hybridization, backcrossing and selection have successfully introgressed a number of desirable traits associated with grain yield, adaptation to abiotic stresses, disease resistance, and bio-fortification of wheat varieties. However, it is time consuming to incorporate genes conferring tolerance/resistance to multiple stresses in a single wheat variety by conventional approaches due to limitations in screening methods and the lower probabilities of combining desirable alleles. Efforts on developing innovative breeding strategies, novel tools and utilizing genetic diversity for new genes/alleles are essential to improve productivity, reduce vulnerability to diseases and pests and enhance nutritional quality. New technologies of high-throughput phenotyping, genome sequencing and genomic selection are promising approaches to maximize progeny screening and selection to accelerate the genetic gains in breeding more productive varieties. Use of cisgenic techniques to transfer beneficial alleles and their combinations within related species also offer great promise especially to achieve durable rust resistance.
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http://dx.doi.org/10.3389/fpls.2016.00991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4933717PMC
July 2016

Genomic prediction for grain zinc and iron concentrations in spring wheat.

Theor Appl Genet 2016 Aug 11;129(8):1595-605. Epub 2016 May 11.

Punjab Agricultural University (PAU), Ludhiana, Punjab, India.

Key Message: Predictability estimated through cross-validation approach showed moderate to high level; hence, genomic selection approach holds great potential for biofortification breeding to enhance grain zinc and iron concentrations in wheat. Wheat (Triticum aestivum L.) is a major staple crop, providing 20 % of dietary energy and protein consumption worldwide. It is an important source of mineral micronutrients such as zinc (Zn) and iron (Fe) for resource poor consumers. Genomic selection (GS) approaches have great potential to accelerate development of Fe- and Zn-enriched wheat. Here, we present the results of large-scale genomic and phenotypic data from the HarvestPlus Association Mapping (HPAM) panel consisting of 330 diverse wheat lines to perform genomic predictions for grain Zn (GZnC) and Fe (GFeC) concentrations, thousand-kernel weight (TKW) and days to maturity (DTM) in wheat. The HPAM lines were phenotyped in three different locations in India and Mexico in two successive crop seasons (2011-12 and 2012-13) for GZnC, GFeC, TKW and DTM. The genomic prediction models revealed that the estimated prediction abilities ranged from 0.331 to 0.694 for Zn and from 0.324 to 0.734 for Fe according to different environments, whereas prediction abilities for TKW and DTM were as high as 0.76 and 0.64, respectively, suggesting that GS holds great potential in biofortification breeding to enhance grain Zn and Fe concentrations in bread wheat germplasm.
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http://dx.doi.org/10.1007/s00122-016-2726-yDOI Listing
August 2016

Zinc and iron concentration QTL mapped in a Triticum spelta × T. aestivum cross.

Theor Appl Genet 2014 Jul 28;127(7):1643-51. Epub 2014 May 28.

Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India.

Key Message: Ten QTL underlying the accumulation of Zn and Fe in the grain were mapped in a set of RILs bred from the cross Triticum spelta × T. aestivum . Five of these loci (two for Zn and three for Fe) were consistently detected across seven environments. The genetic basis of accumulation in the grain of Zn and Fe was investigated via QTL mapping in a recombinant inbred line (RIL) population bred from a cross between Triticum spelta and T. aestivum. The concentration of the two elements was measured from grain produced in three locations over two consecutive cropping seasons and from a greenhouse trial. The range in Zn and Fe concentration across the RILs was, respectively, 18.8-73.5 and 25.3-59.5 ppm, and the concentrations of the two elements were positively correlated with one another (rp =+0.79). Ten QTL (five each for Zn and Fe accumulation) were detected, mapping to seven different chromosomes. The chromosome 2B and 6A grain Zn QTL were consistently expressed across environments. The proportion of the phenotype explained (PVE) by QZn.bhu-2B was >16 %, and the locus was closely linked to the SNP marker 1101425|F|0, while QZn.bhu-6A (7.0 % PVE) was closely linked to DArT marker 3026160|F|0. Of the five Fe QTL detected, three, all mapping to chromosome 1A were detected in all seven environments. The PVE for QFe.bhu-3B was 26.0 %.
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http://dx.doi.org/10.1007/s00122-014-2327-6DOI Listing
July 2014

The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production.

Annu Rev Phytopathol 2011 ;49:465-81

International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.

Race Ug99 of the fungus Puccinia graminis tritici that causes stem or black rust disease on wheat was first detected in Uganda in 1998. Seven races belonging to the Ug99 lineage are now known and have spread to various wheat-growing countries in the eastern African highlands, as well as Zimbabwe, South Africa, Sudan, Yemen, and Iran. Because of the susceptibility of 90% of the wheat varieties grown worldwide, the Ug99 group of races was recognized as a major threat to wheat production and food security. Its spread, either wind-mediated or human-aided, to other countries in Africa, Asia, and beyond is evident. Screening in Kenya and Ethiopia has identified a low frequency of resistant wheat varieties and breeding materials. Identification and transfer of new sources of race-specific resistance from various wheat relatives is underway to enhance the diversity of resistance. Although new Ug99-resistant varieties that yield more than current popular varieties are being released and promoted, major efforts are required to displace current Ug99 susceptible varieties with varieties that have diverse race-specific or durable resistance and mitigate the Ug99 threat.
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http://dx.doi.org/10.1146/annurev-phyto-072910-095423DOI Listing
August 2013