Genome‐Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

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 Unravels LRK1 as a Dark Respiration Regulator in Rice (Oryza sativa L.)

International Journal of Molecular Sciences ◽

10.3390/ijms21144930 ◽

2020 ◽

Vol 21 (14) ◽

pp. 4930

Author(s):

Mingnan Qu ◽

Jemaa Essemine ◽

Ming Li ◽

Shuoqi Chang ◽

Tiangen Chang ◽

...

Keyword(s):

Oryza Sativa ◽

Association Study ◽

Natural Variation ◽

Genome Wide Association Study ◽

Oryza Sativa L ◽

Dark Respiration ◽

Genome Wide Association ◽

Strong Positive Correlation ◽

Diversity Panel ◽

Genome Wide

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (Rd) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with Rd. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that Rd shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. Rd also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of Rd collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high Rd. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% Rd of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of Rd in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.

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Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.)

The Plant Genome ◽

10.1002/tpg2.20006 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Xiping Yang ◽

Ziliang Luo ◽

James Todd ◽

Sushma Sood ◽

Jianping Wang

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Yield Traits ◽

Saccharum Spp ◽

Diversity Panel ◽

Genome Wide

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An approach based on a genome-wide association study reveals candidate loci for narcolepsy

Human Genetics ◽

10.1007/s00439-010-0862-z ◽

2010 ◽

Vol 128 (4) ◽

pp. 433-441 ◽

Cited By ~ 24

Author(s):

Mihoko Shimada ◽

Taku Miyagawa ◽

Minae Kawashima ◽

Susumu Tanaka ◽

Yutaka Honda ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Candidate Loci

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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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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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