Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses

Long, Yan; Hofmann, Nicolle E.; Li, Shuxian; Ferreira, Márcio Elias; Song, Baoxing; Jiang, Guang‐Zhen; Ren, Shuxin; Quigley, Charles V.; Fickus, E. W.; Cregan, Perry B.; Song, Qijian

doi:10.1186/s12864-017-3922-0

Cited by 67 publications

(65 citation statements)

References 47 publications

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“…This could be explained by high phenotypic variance of these studied traits (Gibson, 2012;Korte and Farlow, 2013). Yan et al (2017) also stated that increasing the frequency of the genotypes containing causative alleles would increase the chance of detecting a variant with major effects. The G.…”

Section: Correlations Among Traitsmentioning

confidence: 99%

Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Large

Taliercio

et al. 2019

Crop Science

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The relatively low genetic variation of current US soybean [Glycine max (L.) Merr.] cultivars constrains the improvement of grain yield and other agronomic and seed composition traits. Recently, a substantial effort has been undertaken to introduce novel genetic diversity present in wild soybean (Glycine soja Siebold & Zucc.) into elite cultivars, in both public and private breeding programs. The objectives of this research were to evaluate the phenotypic diversity within a collection of 80 G. soja plant introductions (PIs) in the USDA National Genetic Resources Program and to analyze the correlations between agronomic and seed composition traits. Field tests were conducted in Missouri and North Carolina during 3 yr (2013, 2014, and 2015) in a randomized complete block design. The phenotypic data collected included plant maturity date, seed weight, and the seed concentration of protein, oil, essential amino acids, fatty acid, and soluble carbohydrates. We found that genotype was a significant (P < 0.0001) source of variation for maturity date, seed weight, seed protein and amino acids, seed oil and fatty acids, and seed carbohydrates, and significant correlations were observed between numerous traits. The G. soja PIs generally had lower seed weight, higher seed contents of protein, linolenic acid, raffinose, and stachyose, and lower seed contents of oil and oleic acid than the cultivated soybean G. max lines. The information and data collected in this study will be invaluable in guiding soybean breeders and geneticists in selecting promising G. soja PIs for research and cultivar improvement.

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Section: Correlations Among Traitsmentioning

confidence: 99%

Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Large

Taliercio

et al. 2019

Crop Science

Self Cite

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“…Molecular markers associated with seed weight have been previously investigated in soybean. GWAS identi ed a total of more than 95 loci controlling seed weight with chromosome 4 harboring 12 loci [1,4,6,7,[11][12][13][14][15][16]. Glyma11g03360, Glyma11g03430, Glyma11g05760, Glyma18g05240, Glyma18g43500, Glyma18g43500, Glyma.03g166700, Glyma.11g164700, Glyma.11g164700, LOC100784416, Glyma05g09390, Glyma.07g076800, Glyma10g28250, Glyma14g08050, Glyma14g08280, Glyma19g33421, Glyma19g33550, and Glyma19g35180 have been reported as potential candidate genes for seed weight in soybean [1,11,12,14].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Ravelombola¹,

Qin²,

Shi³

et al. 2020

Preprint

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BackgroundSoybean [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 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). Population structure was inferred using STRUCTURE 2.3.4, 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 (if no annotated genes found close the top one) 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 in soybean through marker-assisted selection (MAS) and GS in breeding programs. After validation, the candidate genes can be transferred to new cultivars using the linked 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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“…GWAS overcomes all the drawbacks of QTL mapping, and the identified markers through this approach can be used for any population [12]. GWAS has been successfully carried out for the common bean in order to elucidate marker-trait association for agronomic traits [13], seed weight [14], disease resistance [15], cooking properties [16], anthracnose resistance [17], and drought tolerance [18]. These studies resulted in the identification of some candidate genes that can be helpful in the development of new genetic stocks for breeding perspectives in the common bean.…”

Section: Introductionmentioning

confidence: 99%

Uncovering Phenotypic Diversity and DArTseq Marker Loci Associated with Antioxidant Activity in Common Bean

Nadeem

Gündoğdu

Erċışlı

et al. 2019

Genes

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Antioxidants play an important role in animal and plant life owing to their involvement in complex metabolic and signaling mechanisms, hence uncovering the genetic basis associated with antioxidant activity is very important for the development of improved varieties. Here, a total of 182 common bean (Phaseolus vulgaris) landraces and six commercial cultivars collected from 19 provinces of Turkey were evaluated for seed antioxidant activity under four environments and two locations. Antioxidant activity was measured using ABTS radical scavenging capacity and mean antioxidant activity in common bean landraces was 20.03 µmol TE/g. Analysis of variance reflected that genotype by environment interaction was statistically non-significant and heritability analysis showed higher heritability of antioxidant activity. Variations in seed color were observed, and a higher antioxidant activity was present in seeds having colored seed as compared to those having white seeds. A negative correlation was found between white-colored seeds and antioxidant activity. A total of 7900 DArTseq markers were used to explore the population structure that grouped the studied germplasm into two sub-populations on the basis of their geographical origins and trolox equivalent antioxidant capacity contents. Mean linkage disequilibrium (LD) was 54%, and mean Genes 2020, 11, 36 2 of 17 LD decay was 1.15 Mb. Mixed linear model i.e., the Q + K model demonstrated that four DArTseq markers had significant association (p < 0.01) for antioxidant activity. Three of these markers were present on chromosome Pv07, while the fourth marker was located on chromosome Pv03. Among the identified markers, DArT-3369938 marker showed maximum (14.61%) variation. A total of four putative candidate genes were predicted from sequences reflecting homology to identified DArTseq markers. This is a pioneering study involving the identification of association for antioxidant activity in common bean seeds. We envisage that this study will be very helpful for global common bean breeding community in order to develop cultivars with higher antioxidant activity.

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Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses

Cited by 67 publications

References 47 publications

Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Characterization of Select Wild Soybean Accessions in the USDA Germplasm Collection for Seed Composition and Agronomic Traits

Genome-wide association study and genomic selection for plant height, maturity, seed weight, and yield in soybean

Uncovering Phenotypic Diversity and DArTseq Marker Loci Associated with Antioxidant Activity in Common Bean

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