Mapping QTLs for plant height and flowering time in a Chinese summer planting soybean RIL population

Cao, Yongce; Li, Shuguang; He, Xiaohong; Chang, Fangguo; Kong, Jiejie; Gai, Junyi; Zhao, Tuanjie

doi:10.1007/s10681-016-1834-8

Cited by 31 publications

(39 citation statements)

References 62 publications

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“…Plant height and NN are complex traits governed by many quantitative trait loci (QTL) in soybeans ( Lee et al, 1996 ; Zhang et al, 2004 ; Liu et al, 2011 , 2013 ; Yao et al, 2015 ; Cao et al, 2017 ). To date, more than 200 and 30 QTLs for PH and NN have been reported on SoyBase 1 via linkage mapping.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Studies for Dynamic Plant Height and Number of Nodes on the Main Stem in Summer Sowing Soybeans

et al. 2018

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Plant height (PH) and the number of nodes on the main stem (NN) serve as major plant architecture traits affecting soybean seed yield. Although many quantitative trait loci for the two traits have been reported, their genetic controls at different developmental stages in soybeans remain unclear. Here, 368 soybean breeding lines were genotyped using 62,423 single nucleotide polymorphism (SNP) markers and phenotyped for the two traits at three different developmental stages over two locations in order to identify their quantitative trait nucleotides (QTNs) using compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) approaches. As a result, 11 and 13 QTNs were found by CMLM to be associated with PH and NN, respectively. Among these QTNs, 8, 3, and 4 for PH and 6, 6, and 8 for NN were found at the three stages, and 3 and 6 were repeatedly detected for PH and NN. In addition, 34 and 30 QTNs were found by mrMLM to be associated with PH and NN, respectively. Among these QTNs, 11, 13, and 16 for PH and 11, 15, and 8 for NN were found at the three stages. A majority of these QTNs overlapped with the previously reported loci. Moreover, one QTN within the known E2 locus for flowering time was detected for the two traits at all three stages, and another that overlapped with the Dt1 locus for stem growth habit was also identified for the two traits at the mature stage. This may explain the highly significant correlation between the two traits. Our findings provide evidence for mixed major plus polygenes inheritance for dynamic traits and an extended understanding of their genetic architecture for molecular dissection and breeding utilization in soybeans.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Studies for Dynamic Plant Height and Number of Nodes on the Main Stem in Summer Sowing Soybeans

et al. 2018

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“…High density genetic maps are critical to improving the accuracy and resolution of QTL mapping, even with low-heritability quantitative traits ( Song et al 2016 , Cao et al 2017 ). In our study, BARCSoySNP6K iSelect BeadChip was used to develop high-density linkage maps for the two RIL populations, and to anchor QTL to small genetic regions.…”

Section: Discussionmentioning

confidence: 99%

Mapping Quantitative Trait Loci for Tolerance to Pythium irregulare in Soybean (Glycine max L.)

Lin

Wani

Collins

et al. 2018

G3 Genes|Genomes|Genetics

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Pythium root rot is one of the significant diseases of soybean (Glycine max (L.) Merr.) in the United States. The causal agent of the disease is a soil-borne oomycete pathogen Pythium irregulare, the most prevalent and aggressive species of Pythium in North Central United States. However, few studies have been conducted in soybean for the identification of quantitative trait loci (QTL) for tolerance to P. irregulare. In this study, two recombinant inbred line (RIL) populations (designated as POP1 and POP2) were challenged with P. irregulare (isolate CMISO2-5-14) in a greenhouse assay. POP1 and POP2 were derived from ‘E09014’ × ‘E05226-T’ and ‘E05226-T’ × ‘E09088’, and contained 113 and 79 lines, respectively. Parental tests indicated that ‘E05226-T’ and ‘E09014’ were more tolerant than ‘E09088’, while ‘E09088’ was highly susceptible to the pathogen. The disease indices, root weight of inoculation (RWI) and ratio of root weight (RRW) of both populations showed near normal distributions, with transgressive segregation, suggesting the involvement of multiple QTL from both parents contributed to the tolerance. All the lines were genotyped using Illumina Infinium BARCSoySNP6K iSelect BeadChip and yielded 1373 and 1384 polymorphic markers for POP1 and POP2, respectively. Notably, despite high density, polymorphic markers coverage was incomplete in some genomic regions. As such, 28 and 37 linkage groups were obtained in POP1 and POP2, respectively corresponding to the 20 soybean chromosomes. Using RRW, one QTL was identified in POP1 on Chromosome 20 that explained 12.7–13.3% of phenotypic variation. The desirable allele of this QTL was from ‘E05226-T’. Another QTL was found in POP2 on Chromosome 11. It explained 15.4% of the phenotypic variation and the desirable allele was from ‘E09088’. However, no QTL were identified using RWI in either population. These results supported that RRW was more suitable to be used to evaluate P. irregulare tolerance in soybean.

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“…Genome-wide association study (GWAS) and genomic selection (GS) are powerful tools to assist with understanding the genetic architecture governing complex traits of importance in agriculture. GWAS has been conducted to identify markers associated with agronomic traits in soybean [2,3]. To date, more than 60 loci found through GWAS have been reported to be associated with maturity in soybean [4][5][6][7][8][9].…”

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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Mapping QTLs for plant height and flowering time in a Chinese summer planting soybean RIL population

Cited by 31 publications

References 62 publications

Genome-Wide Association Studies for Dynamic Plant Height and Number of Nodes on the Main Stem in Summer Sowing Soybeans

Genome-Wide Association Studies for Dynamic Plant Height and Number of Nodes on the Main Stem in Summer Sowing Soybeans

Mapping Quantitative Trait Loci for Tolerance to Pythium irregulare in Soybean (Glycine max L.)

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

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