Identification of Additive–Epistatic QTLs Conferring Seed Traits in Soybean Using Recombinant Inbred Lines

Li, Meng; Zeng, Jian; Razzaq, Muhammad Khuram; Xu, Xianchao; Xu, Yufei; Wang, Wubin; He, Jianbo; Xing, Guangnan; Gai, Junyi

doi:10.3389/fpls.2020.566056

Cited by 15 publications

(9 citation statements)

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“…Seed size and shape traits in soybean are highly complex and controlled by many loci as demonstrated in the earlier QTL mapping studies (Xu et al, 2011;Hu et al, 2013;Niu et al, 2013;Hina et al, 2020). Several QTLs for seed size and shape traits have been previously identified in soybean using bi-parental mapping (Hoeck et al, 2003;Salas et al, 2006;Xu et al, 2011;Hu et al, 2013;Che et al, 2014;Kato et al, 2014;Liang et al, 2016;Fang et al, 2017;Yang et al, 2017;Fujii et al, 2018;Cui et al, 2020;Hina et al, 2020;Li et al, 2020). Genome-wide association studies were also attempted to identify QTLs for seed size and shape traits in soybean (Hu et al, 2013;Niu et al, 2013;Fang et al, 2017;Li et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…In soybean, QTLs for seed size and shape traits have been identified using simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers (Hoeck et al, 2003;Salas et al, 2006;Xu et al, 2011;Hu et al, 2013;Niu et al, 2013;Kato et al, 2014;Liang et al, 2016;Fang et al, 2017;Yang et al, 2017;Fujii et al, 2018;Li et al, 2019Li et al, , 2020Cui et al, 2020;Hina et al, 2020). Many QTLs have been identified for seed size and shape traits in soybean, but our understanding of their genetic architecture for practical application in soybean breeding is still limited because most of the QTLs are population and environment specific (Hina et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population

Kumawat

2021

Front. Genet.

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Seed size and shape traits are important determinants of seed yield and appearance quality in soybean [Glycine max (L.) Merr.]. Understanding the genetic architecture of these traits is important to enable their genetic improvement through efficient and targeted selection in soybean breeding, and for the identification of underlying causal genes. To map seed size and shape traits in soybean, a recombinant inbred line (RIL) population developed from K099 (small seed size) × Fendou 16 (large seed size), was phenotyped in three growing seasons. A genetic map of the RIL population was developed using 1,485 genotyping by random amplicon sequencing-direct (GRAS-Di) and 177 SSR markers. Quantitative trait locus (QTL) mapping was conducted by inclusive composite interval mapping. As a result, 53 significant QTLs for seed size traits and 27 significant QTLs for seed shape traits were identified. Six of these QTLs (qSW8.1, qSW16.1, qSLW2.1, qSLT2.1, qSWT1.2, and qSWT4.3) were identified with LOD scores of 3.80–14.0 and R2 of 2.36%–39.49% in at least two growing seasons. Among the above significant QTLs, 24 QTLs were grouped into 11 QTL clusters, such as, three major QTLs (qSL2.3, qSLW2.1, and qSLT2.1) were clustered into a major QTL on Chr.02, named as qSS2. The effect of qSS2 was validated in a pair of near isogenic lines, and its candidate genes (Glyma.02G269400, Glyma.02G272100, Glyma.02G274900, Glyma.02G277200, and Glyma.02G277600) were mined. The results of this study will assist in the breeding programs aiming at improvement of seed size and shape traits in soybean.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population

Kumawat

2021

Front. Genet.

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“…(2020) found 88 main and epistatic-effect QTLs. Similarly, 42 additive effect QTLs for seed traits were mapped by Li et al. (2020) .…”

Section: Introductionmentioning

confidence: 99%

Identification of quantitative trait loci (QTLs) and candidate genes for seed shape and 100-seed weight in soybean [Glycine max (L.) Merr.]

et al. 2023

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Seed size and shape are important traits determining yield and quality in soybean. Seed size and shape are also desirable for specialty soy foods like tofu, natto, miso, and edamame. In order to find stable quantitative trait loci (QTLs) and candidate genes for seed shape and 100-seed weight, the current study used vegetable type and seed soybean-derived F2 and F2:3 mapping populations. A total of 42 QTLs were mapped, which were dispersed across 13 chromosomes. Of these, seven were determined to be stable QTLs and five of them were major QTLs, namely qSL-10-1, qSW-4-1, qSV-4-1, qSLW-10-1, and qSLH-10-1. Thirteen of the 42 QTLs detected in the current study were found at known loci, while the remaining 29 were discovered for the first time. Out of these 29 novel QTLs, 17 were major QTLs. Based on Protein Analysis Through Evolutionary Relationships (PANTHER), gene annotation information, and literature search, 66 genes within seven stable QTLs were predicted to be possible candidate genes that might regulate seed shape and seed weight in soybean. The current study identified the key candidate genes and quantitative trait loci (QTLs) controlling soybean seed shape and weight, and these results will be very helpful in marker-assisted breeding for developing soybean varieties with improved seed weight and desired seed shape.

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“…There is great variation in soybean 100-seed weight, ranging from 7.30 to 23.60 g and from 5.64 to 34.80 g in the germplasm collections from the USA and China, respectively (Zhang et al 2016 ; Zhao et al 2019 ). The quantitative trait loci (QTL) controlling 100-seed weight have been identified by genome-wide association studies (GWAS) (Fang et al 2017 ; Hao et al 2012 ; Karikari et al 2020 ; Li et al 2019b ; Zhang et al 2016 , 2015b ) and linkage mapping (Han et al 2012 ; Hoeck et al 2003 ; Karikari et al 2019 ; Kato et al 2014 ; Kim et al 2010 ; Li et al 2020 ; Liu et al 2007 ; Lu et al 2017 ; Panthee et al 2005 ; Teng et al 2009 ; Yan et al 2017 ; Yang et al 2019 ). However, many QTL for 100-seed weight were mapped to relatively large genomic regions, due to low-density markers, small mapping population size, or lack of recombination, which causes difficulties to identify candidate genes in these regions.…”

Section: Introductionmentioning

confidence: 99%

Identification of major quantitative trait loci and candidate genes for seed weight in soybean

Kong

Miao

et al. 2023

Theor Appl Genet

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Key message Four major quantitative trait loci for 100-seed weight were identified in a soybean RIL population under five environments, and the most likely candidate genes underlying these loci were identified. Abstract Seed weight is an important target of soybean breeding. However, the genes underlying the major quantitative trait loci (QTL) controlling seed weight remain largely unknown. In this study, a soybean population of 300 recombinant inbred lines (RILs) derived from a cross between PI595843 (PI) and WH was used to map the QTL and identify candidate genes for seed weight. The RIL population was genotyped through whole genome resequencing, and phenotyped for 100-seed weight under five environments. A total of 38 QTL were detected, and four major QTL, each explained at least 10% of the variation in 100-seed weight, were identified. Six candidate genes within these four major QTL regions were identified by analyses of their tissue expression patterns, gene annotations, and differential gene expression levels in soybean seeds during four developmental stages between two parental lines. Further sequence variation analyses revealed a C to T substitution in the first exon of the Glyma.19G143300, resulting in an amino acid change between PI and WH, and thus leading to a different predicted kinase domain, which might affect its protein function. Glyma.19G143300 is highly expressed in soybean seeds and encodes a leucine-rich repeat receptor-like protein kinase (LRR-RLK). Its predicted protein has typical domains of LRR-RLK family, and phylogenetic analyses reveled its similarity with the known LRR-RLK protein XIAO (LOC_Os04g48760), which is involved in controlling seed size. The major QTL and candidate genes identified in this study provide useful information for molecular breeding of new soybean cultivars with desirable seed weight.

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Identification of Additive–Epistatic QTLs Conferring Seed Traits in Soybean Using Recombinant Inbred Lines

Cited by 15 publications

References 47 publications

A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population

A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population

Identification of quantitative trait loci (QTLs) and candidate genes for seed shape and 100-seed weight in soybean [Glycine max (L.) Merr.]

Identification of major quantitative trait loci and candidate genes for seed weight in soybean

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