Genome‐wide Association Study of Agronomic Traits in a Spring‐Planted North American Elite Hard Red Spring Wheat Panel

Abstract Background Soybean [ Glycine max (L.) Merr.] is a legume of great interest worldwide. Enhancing genetic gain for agronomic traits via molecular approaches has been long considered as the main task for soybean breeders and geneticists. The objectives of this study were to evaluate maturity, plant height, seed weight, and yield in a diverse soybean accession panel, to conduct a genome-wide association study (GWAS) for these traits and identify SNP markers associated with the four traits, and to assess genomic selection (GS) accuracy. Results A total of 250 soybean accessions were evaluated for maturity, plant height, seed weight, and yield over three years. This panel was genotyped with a total of 10,259 high quality SNPs postulated from genotyping by sequencing (GBS). GWAS was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model, and GS was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that a total of 20, 31, 37, 31, and 23 SNPs were significantly associated with the average 3-year data for maturity, plant height, seed weight, and yield, respectively; some significant SNPs were mapped into previously described loci ( E2 , E4 , and Dt1 ) affecting maturity and plant height in soybean and a new locus mapped on chromosome 20 was significantly associated with plant height; Glyma.10g228900 , Glyma.19g200800 , Glyma.09g196700 , and Glyma.09g038300 were candidate genes found in the vicinity of the top or the second best SNP for maturity, plant height, seed weight, and yield, respectively; a 11.5-Mb region of chromosome 10 was associated with both seed weight and yield; and GS accuracy was trait-, year-, and population structure-dependent. Conclusions The SNP markers identified from this study for plant height, maturity, seed weight and yield can be used to improve the four agronomic traits through marker-assisted selection (MAS) and GS in soybean breeding programs. After validation, the candidate genes can be transferred to new cultivars using SNP markers through MAS. The high GS accuracy has confirmed that the four agronomic traits can be selected in molecular breeding through GS.

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Genome-Wide Association Study Identifying Candidate Genes Influencing Important Agronomic Traits of Flax (Linum usitatissimum L.) Using SLAF-seq

Frontiers in Plant Science ◽

10.3389/fpls.2017.02232 ◽

2018 ◽

Vol 8 ◽

Cited By ~ 10

Author(s):

Dongwei Xie ◽

Zhigang Dai ◽

Zemao Yang ◽

Jian Sun ◽

Debao Zhao ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Linum Usitatissimum ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genome Wide Association ◽

Linum Usitatissimum L ◽

Genome Wide

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Genome-wide association study for agronomic and physiological traits in spring wheat evaluated in a range of heat prone environments

Theoretical and Applied Genetics ◽

10.1007/s00122-017-2927-z ◽

2017 ◽

Vol 130 (9) ◽

pp. 1819-1835 ◽

Cited By ~ 41

Author(s):

Francis C. Ogbonnaya ◽

Awais Rasheed ◽

Emeka C. Okechukwu ◽

Abdulqader Jighly ◽

Farid Makdis ◽

...

Keyword(s):

Association Study ◽

Spring Wheat ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Physiological Traits ◽

Genome Wide

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Effect of Population Size on Genome-Wide Association Study of Agronomic Traits in Soybean

Proceedings of the Latvian Academy of Sciences Section B Natural Exact and Applied Sciences ◽

10.2478/prolas-2020-0039 ◽

2020 ◽

Vol 74 (4) ◽

pp. 244-251

Author(s):

Alibek Zatybekov ◽

Yerlan Turuspekov ◽

Botakoz Doszhanova ◽

Svetlana Didorenko ◽

Saule Abugalieva

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Single Nucleotide Polymorphism Array ◽

Field Trials ◽

Genome Wide Association ◽

Medium Size ◽

Polymorphic Snps ◽

Genome Wide ◽

Size Population

AbstractSoybean is increasingly becoming one of the main oilseeds crops in Kazakhstan, with a major growing area in the south-eastern part of the country. The comparative assessment of small-size (108) and medium-size (276 accessions) collections of soybean originated from five regions of the world was made in field trials in Almaty region (south-east of Kazakhstan). The full collection was genotyped using the Illumina iSelect 6K SNP (single nucleotide polymorphism) array that allowed observation of 4651 polymorphic SNPs. The genome-wide association study (GWAS) was conducted using the following six important agronomic traits: flowering time, seed maturation time, plant height, number of fertile nodes, number of seeds per node, and thousand seed weight. In total, GWAS using TASSEL package identified 56 stable QTNs (quantitative trait nucleotdies) for all the studied traits, including 42 QTNs detected using the medium-size collection. It was shown that the medium-size population, in comparison with the small-size population, was preferable for the detection of significant associations. A comparative analysis of the data with previously published results suggested that 36 of the stable 56 QTNs were presumably novel associations. The revealed QTNs can be used in the molecular breeding projects for soybean yield improvement.

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Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

10.21203/rs.3.rs-859874/v1 ◽

2021 ◽

Author(s):

Dong Cao ◽

Dongxia Wang ◽

Shiming Li ◽

Yun Li ◽

Ming Hao ◽

...

Keyword(s):

Genetic Diversity ◽

Association Study ◽

Genome Wide Association Study ◽

Agronomic Traits ◽

Genotyping By Sequencing ◽

Genome Wide Association ◽

Energy Crop ◽

Hexaploid Triticale ◽

Genome Wide ◽

Genetic Mechanisms

Abstract Key message The genetic diversity and loci underlying agronomic traits were analysed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.Abstract Triticale (×Triticosecale Wittmack) is an economically important grain-forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.

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