800 results match your criteria breeding genotyping-by-sequencing

Characterization and Mapping of Spot Blotch in Introgression Lines Using SNP Markers.

Front Plant Sci 2021 28;12:650400. Epub 2021 May 28.

School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.

Spot blotch (SB) of wheat is emerging as a major threat to successful wheat production in warm and humid areas of the world. SB, also called leaf blight, is caused by , and is responsible for high yield losses in Eastern Gangetic Plains Zone in India. More recently, SB is extending gradually toward cooler, traditional wheat-growing North-Western part of the country which is a major contributor to the national cereal basket. Read More

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Dissection of the Genetic Basis of Yield-Related Traits in the Chinese Peanut Mini-Core Collection Through Genome-Wide Association Studies.

Front Plant Sci 2021 20;12:637284. Epub 2021 May 20.

Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.

Peanut is an important legume crop worldwide. To uncover the genetic basis of yield features and assist breeding in the future, we conducted genome-wide association studies (GWAS) for six yield-related traits of the Chinese peanut mini-core collection. The seed (pod) size and weight of the population were investigated under four different environments, and these traits showed highly positive correlations in pairwise combinations. Read More

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High-resolution genome-wide association study and genomic prediction for disease resistance and cold tolerance in wheat.

Theor Appl Genet 2021 Jun 1. Epub 2021 Jun 1.

State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.

Key Message: High-resolution genome-wide association study (GWAS) facilitated QTL fine mapping and candidate gene identification, and the GWAS based genomic prediction models were highly predictive and valuable in wheat genomic breeding. Wheat is a major staple food crop and provides more than one-fifth of the daily calories and dietary proteins for humans. Genome-wide association study (GWAS) and genomic selection (GS) for wheat stress resistance and tolerance related traits are critical to understanding their genetic architecture for improvement of breeding selection efficiency. Read More

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Identification of QTLs for Spot Blotch Resistance in Two Bi-Parental Mapping Populations of Wheat.

Plants (Basel) 2021 May 13;10(5). Epub 2021 May 13.

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

Spot blotch (SB) disease caused by the hemibiotrophic pathogen inflicting major losses to the wheat grown in warm and highly humid areas of the Indian subcontinent, including Bangladesh, necessitates identification of QTLs stably expressing in Indian subcontinent conditions. Thus, two RIL mapping populations, i.e. Read More

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Genome-wide association mapping of the 'super-soft' kernel texture in white winter wheat.

Theor Appl Genet 2021 May 30. Epub 2021 May 30.

USDA-ARS Western Wheat Quality Laboratory, E-202 Food Quality Building, Washington State University, Pullman, WA, 99164-6394, USA.

Key Message: The novel super-soft kernel phenotype has the potential to improve wheat processing and flour quality. We identified genomic regions associated with this kernel texture in white winter wheat. Grain hardness is a key determinant of wheat milling and baking quality. Read More

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Genetic mapping and identification of a QTL determining tolerance to freezing stress in Fragaria vesca L.

PLoS One 2021 21;16(5):e0248089. Epub 2021 May 21.

Department of Genetics, Genomics and Breeding, NIAB-EMR, East Malling, Kent, United Kingdom.

Extreme cold and frost cause significant stress to plants which can potentially be lethal. Low temperature freezing stress can cause significant and irreversible damage to plant cells and can induce physiological and metabolic changes that impact on growth and development. Low temperatures cause physiological responses including winter dormancy and autumn cold hardening in strawberry (Fragaria) species, and some diploid F. Read More

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Construction of a high density genetic map for hexaploid kiwifruit (Actinidia chinensis var. deliciosa) using genotyping by sequencing.

G3 (Bethesda) 2021 May 1. Epub 2021 May 1.

Plant & Food Research, Palmerston North, New Zealand.

Commercially grown kiwifruit (genus Actinidia) are generally of two sub-species which have a base haploid genome of 29 chromosomes. The yellow-fleshed A. chinensis var. Read More

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Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.).

BMC Genomics 2021 May 17;22(1):356. Epub 2021 May 17.

Department of Plant and Environmental Sciences, New Mexico State University, NM, 88003, Las Cruces, USA.

Background: Chile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Read More

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Genome-wide association study reveals novel loci associated with feeding behavior in Pekin ducks.

BMC Genomics 2021 May 8;22(1):334. Epub 2021 May 8.

National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.

Background: Feeding behavior traits are an essential part of livestock production. However, the genetic base of feeding behavior traits remains unclear in Pekin ducks. This study aimed to determine novel loci related to feeding behavior in Pekin ducks. Read More

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Untargeted metabotyping to study phenylpropanoid diversity in crop plants.

Physiol Plant 2021 May 7. Epub 2021 May 7.

Leibniz Institute for Plant Genetics and Crop Plant Research, Gatersleben, Germany.

Plant genebanks constitute a key resource for breeding to ensure crop yield under changing environmental conditions. Because of their roles in a range of stress responses, phenylpropanoids are promising targets. Phenylpropanoids comprise a wide array of metabolites; however, studies regarding their diversity and the underlying genes are still limited for cereals. Read More

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Marker-Assisted Introgression and Stacking of Major QTLs Controlling Grain Number () and Number of Primary Branching () to NERICA Cultivars.

Plants (Basel) 2021 Apr 22;10(5). Epub 2021 Apr 22.

Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.

The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of them were cloned, only a few were utilized for actual systematic introgression breeding programs. Read More

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Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron.

Plants (Basel) 2021 Apr 19;10(4). Epub 2021 Apr 19.

Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.

Excess soluble iron in acidic soil is an unfavorable environment that can reduce rice production. To better understand the tolerance mechanism and identify genetic loci associated with iron toxicity (FT) tolerance in a highly diverse indica Thai rice population, a genome-wide association study (GWAS) was performed using genotyping by sequencing and six phenotypic data (leaf bronzing score (LBS), chlorophyll content, shoot height, root length, shoot biomass, and root dry weight) under both normal and FT conditions. LBS showed a high negative correlation with the ratio of chlorophyll content and shoot biomass, indicating the FT-tolerant accessions can regulate cellular homeostasis when encountering stress. Read More

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Development of an Australian Bread Wheat Nested Association Mapping Population, a New Genetic Diversity Resource for Breeding under Dry and Hot Climates.

Int J Mol Sci 2021 Apr 21;22(9). Epub 2021 Apr 21.

School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia.

Genetic diversity, knowledge of the genetic architecture of the traits of interest and efficient means of transferring the desired genetic diversity into the relevant genetic background are prerequisites for plant breeding. Exotic germplasm is a rich source of genetic diversity; however, they harbor undesirable traits that limit their suitability for modern agriculture. Nested association mapping (NAM) populations are valuable genetic resources that enable incorporation of genetic diversity, dissection of complex traits and providing germplasm to breeding programs. Read More

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Development of whole-genome prediction models to increase the rate of genetic gain in intermediate wheatgrass (Thinopyrum intermedium) breeding.

Plant Genome 2021 Apr 26:e20089. Epub 2021 Apr 26.

Wheat Genetics Resource Center, Dep. of Plant Pathology, Kansas State Univ., 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA.

The development of perennial grain crops is driven by the vision of simultaneous food production and enhanced ecosystem services. Typically, perennial crops like intermediate wheatgrass (IWG)[Thinopyrum intermedium (Host) Barkworth & D.R Dewey] have low seed yield and other detrimental traits. Read More

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High-density mapping for gray leaf spot resistance using two related tropical maize recombinant inbred line populations.

Mol Biol Rep 2021 Apr 22;48(4):3379-3392. Epub 2021 Apr 22.

Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, 650205, China.

Gray leaf spot (GLS) caused by Cercospora zeae-maydis or Cercospora zeina is one of the devastating maize foliar diseases worldwide. Identification of GLS-resistant quantitative trait loci (QTL)/genes plays an urgent role in improving GLS resistance in maize breeding practice. Two groups of recombinant inbred line (RIL) populations derived from CML373 × Ye107 and Chang7-2 × Ye107 were generated and subjected to genotyping-by-sequencing (GBS). Read More

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Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs.

BMC Genomics 2021 Apr 21;22(1):290. Epub 2021 Apr 21.

Animal Genomics, ETH Zürich, Eschikon 27, 8315, Lindau, Switzerland.

Background: The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads.

Results: Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. Read More

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Genetic variation and population structure in China summer maize germplasm.

Sci Rep 2021 Apr 13;11(1):8012. Epub 2021 Apr 13.

Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001, Henan, China.

Maize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. Read More

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The History of Lentil ( subsp. ) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions.

Front Plant Sci 2021 25;12:628439. Epub 2021 Mar 25.

Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal.

Protein-rich legumes accompanied carbohydrate-rich cereals since the beginning of agriculture and yet their domestication history is not as well understood. Lentil ( Medik. subsp. Read More

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Genomic prediction for growth using a low-density SNP panel in dromedary camels.

Sci Rep 2021 Apr 7;11(1):7675. Epub 2021 Apr 7.

Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran.

For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. Read More

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A mutation in Zeaxanthin epoxidase contributes to orange coloration and alters carotenoid contents in pepper fruit (Capsicum annuum).

Plant J 2021 Apr 7. Epub 2021 Apr 7.

Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.

Phytoene synthase (PSY1), capsanthin-capsorubin synthase (CCS), and pseudo-response regulator 2 (PRR2) are three major genes controlling fruit color in pepper (Capsicum spp.). However, the diversity of fruit color in pepper cannot be completely explained by these three genes. Read More

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A genomics resource for genetics, physiology, and breeding of West African sorghum.

Plant Genome 2021 Apr 5:e20075. Epub 2021 Apr 5.

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

Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L. Moench) in western Africa (WA) has diversified across a mosaic of cultures and end uses and along steep precipitation and photoperiod gradients. Read More

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Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F Population of Pepper with Contrasting Powdery Mildew Resistance Trait.

Biomed Res Int 2021 15;2021:6673010. Epub 2021 Mar 15.

Department of Vegetable Crops, Korea National College of Agriculture and Fisheries, Jeonju 54874, Republic of Korea.

Powdery mildew (PM) is a common fungal disease infecting pepper plants worldwide. Molecular breeding of pepper cultivars with powdery mildew resistance is desirable for the economic improvement of pepper cultivation. In the present study, 188 F population derived from AR1 (PM resistant) and TF68 (PM sensitive) parents were subjected to high-throughput genotyping by sequencing (GBS) for the identification of single nucleotide polymorphism (SNP) markers. Read More

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QTL Analysis of Adult Plant Resistance to Stripe Rust in a Winter Wheat Recombinant Inbred Population.

Plants (Basel) 2021 Mar 18;10(3). Epub 2021 Mar 18.

Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA.

Stripe rust, caused by the fungus f. sp. , is a worldwide disease of wheat that causes devastating crop losses. Read More

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Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model.

Int J Mol Sci 2021 Mar 6;22(5). Epub 2021 Mar 6.

Department of Biomedical & Clinical Sciences (BKV), Linköping University, SE-58185 Linköping, Sweden.

A combined Genotyping By Sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) protocol was used to identify-in parallel-genetic variation (Genomic-Wide Association Studies (GWAS) and epigenetic differences of Differentially Methylated Regions (DMR) in the genome of spermatozoa from the porcine animal model. Breeding boars with good semen quality ( = 11) and specific and well-documented differences in fertility (farrowing rate, FR) and prolificacy (litter size, LS) ( = 7) in artificial insemination programs, using combined FR and LS, were categorized as High Fertile (HF, = 4) or Low Fertile (LF, = 3), and boars with Unknown Fertility (UF, = 4) were tested for eventual epigenetical similarity with those fertility-proven. We identified 165,944 Single Nucleotide Polymorphisms (SNPs) that explained 14-15% of variance among selection lines. Read More

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Turbocharging introgression breeding of perennial fruit crops: a case study on apple.

Hortic Res 2020 Apr 1;7(1):47. Epub 2020 Apr 1.

The New Zealand Institute for Plant and Food Research Limited, Hawkes Bay Research Centre, Havelock North, New Zealand.

The allelic diversity of primitive germplasm of fruit crops provides a useful resource for introgressing novel genes to meet consumer preferences and environmental challenges. Pre-breeding facilitates the identification of novel genetic variation in the primitive germplasm and expedite its utilisation in cultivar breeding programmes. Several generations of pre-breeding could be required to minimise linkage drag from the donor parent and to maximise the genomic content of the recipient parent. Read More

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Discovery and fine mapping of Rph28: a new gene conferring resistance to Puccinia hordei from wild barley.

Theor Appl Genet 2021 Mar 28. Epub 2021 Mar 28.

Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia.

Key Message: A new gene Rph28 conferring resistance to barley leaf rust was discovered and fine-mapped on chromosome 5H from wild barley. Leaf rust is a highly destructive disease of barley caused by the fungal pathogen Puccinia hordei. Genetic resistance is considered to be the most effective, economical and eco-friendly approach to minimize losses caused by this disease. Read More

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Dissecting Quantitative Trait Loci for Spot Blotch Resistance in South Asia Using Two Wheat Recombinant Inbred Line Populations.

Front Plant Sci 2021 4;12:641324. Epub 2021 Mar 4.

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

Spot blotch (SB) disease causes significant yield loss in wheat production in the warm and humid regions of the eastern Gangetic plains (EGP) of South Asia (SA). Most of the cultivated varieties in the eastern part of SA are affected by SB under favorable climatic conditions. To understand the nature of SB resistance and map the underlying resistant loci effective in SA, two bi-parental mapping populations were evaluated for 3 years, i. Read More

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Fine Mapping of Leaf Trichome Density Revealed a 747-kb Region on Chromosome 1 in Cold-Hardy Hybrid Wine Grape Populations.

Front Plant Sci 2021 3;12:587640. Epub 2021 Mar 3.

Department of Horticultural Science, University of Minnesota, Twin Cities, MN, United States.

Segregation for leaf trichome density was observed in a cold-hardy hybrid grape population GE1025 ( = ∼125, MN1264 × MN1246) that was previously used to detect a quantitative trait locus (QTL) underlying foliar phylloxera resistance on chromosome 14. Our hypothesis was that high trichome density was associated with resistance to phylloxera. Existing literature found trichome density QTL on chromosomes 1 and 15 using a hybrid grape population of "Horizon" × Illinois 547-1 and suggested a few candidate genes. Read More

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Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color.

Commun Biol 2021 Mar 19;4(1):375. Epub 2021 Mar 19.

Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Read More

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Fine-tuning the performance of ddRAD-seq in the peach genome.

Sci Rep 2021 Mar 18;11(1):6298. Epub 2021 Mar 18.

Laboratorio de Biotecnología, Estación Experimental Agropecuaria (EEA) San Pedro, INTA, 2930, San Pedro, Argentina.

The advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. Read More

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