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

Kumar, Rahul; Saini, Manisha; Taku, Meniari; Debbarma, P.; Mahto, Rohit Kumar; Ramlal, Ayyagari; Sharma, D.R.; Rajendran, Ambika; Pandey, Renu; Gaikwad, Kishor; Lal, S. K.; Talukdar, Akshay

doi:10.3389/fpls.2022.1074245

Cited by 15 publications

(11 citation statements)

References 59 publications

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“…Kumar et al used seed-derived F 2 and F 2:3 of vegetable soybean populations to map QTLs. A total of 42 QTLs were identified, distributed on 13 chromosomes [ 26 ]. For quality traits, a total of 13 QTLs for the traits studied have been mapped on 3 chromosomes of the soybean genome.…”

Section: Discussionmentioning

confidence: 99%

Construction of Genetic Map and QTL Mapping for Seed Size and Quality Traits in Soybean (Glycine max L.)

Gao,

Ma,

et al. 2024

IJMS

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Soybean (Glycine max L.) is the main source of vegetable protein and edible oil for humans, with an average content of about 40% crude protein and 20% crude fat. Soybean yield and quality traits are mostly quantitative traits controlled by multiple genes. The quantitative trait loci (QTL) mapping for yield and quality traits, as well as for the identification of mining-related candidate genes, is of great significance for the molecular breeding and understanding the genetic mechanism. In this study, 186 individual plants of the F2 generation derived from crosses between Changjiangchun 2 and Yushuxian 2 were selected as the mapping population to construct a molecular genetic linkage map. A genetic map containing 445 SSR markers with an average distance of 5.3 cM and a total length of 2375.6 cM was obtained. Based on constructed genetic map, 11 traits including hundred-seed weight (HSW), seed length (SL), seed width (SW), seed length-to-width ratio (SLW), oil content (OIL), protein content (PRO), oleic acid (OA), linoleic acid (LA), linolenic acid (LNA), palmitic acid (PA), stearic acid (SA) of yield and quality were detected by the multiple- d size traits and 113 QTLs related to quality were detected by the multiple QTL model (MQM) mapping method across generations F2, F2:3, F2:4, and F2:5. A total of 71 QTLs related to seed size traits and 113 QTLs related to quality traits were obtained in four generations. With those QTLs, 19 clusters for seed size traits and 20 QTL clusters for quality traits were summarized. Two promising clusters, one related to seed size traits and the other to quality traits, have been identified. The cluster associated with seed size traits spans from position 27876712 to 29009783 on Chromosome 16, while the cluster linked to quality traits spans from position 12575403 to 13875138 on Chromosome 6. Within these intervals, a reference genome of William82 was used for gene searching. A total of 36 candidate genes that may be involved in the regulation of soybean seed size and quality were screened by gene functional annotation and GO enrichment analysis. The results will lay the theoretical and technical foundation for molecularly assisted breeding in soybean.

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Section: Discussionmentioning

confidence: 99%

Construction of Genetic Map and QTL Mapping for Seed Size and Quality Traits in Soybean (Glycine max L.)

Gao,

Ma,

et al. 2024

IJMS

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“…Seed size, oil and protein contents are complex traits controlled by genetic and environmental factors during seed development and maturation. Given their importance in soybean breeding, researchers have performed extensive linkage analysis to identify quantitative trait loci (QTL) associated with these three seed traits using various bi-parental derived populations, such as F2 population, recombinant inbred lines (RILs), chromosome segment substitution lines (CSSLs), and near-isogenic lines (NILs) ( Han et al., 2012 ; Eskandari et al., 2013a ; Eskandari et al., 2013b ; Qi et al., 2014 ; Warrington et al., 2015 ; Wang et al., 2015a ; Yang et al., 2019 ; Cui et al., 2020 ; Kumawat and Xu, 2021 ; Kumar et al., 2022 ; Luo et al., 2022 ; Yang et al., 2022b ). So far, hundreds of QTLs related to seed size (including seed weight), oil accumulation, and protein content have been documented in the SoyBase Genome Database ( http://www.soybase.org ).…”

Section: Genetic Mapping Associated With Seed Size Oil and Protein Co...mentioning

confidence: 99%

Genetic regulatory networks of soybean seed size, oil and protein contents

Duan

Li²,

Wang³

et al. 2023

Front. Plant Sci.

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As a leading oilseed crop that supplies plant oil and protein for daily human life, increasing yield and improving nutritional quality (high oil or protein) are the top two fundamental goals of soybean breeding. Seed size is one of the most critical factors determining soybean yield. Seed size, oil and protein contents are complex quantitative traits governed by genetic and environmental factors during seed development. The composition and quantity of seed storage reserves directly affect seed size. In general, oil and protein make up almost 60% of the total storage of soybean seed. Therefore, soybean’s seed size, oil, or protein content are highly correlated agronomical traits. Increasing seed size helps increase soybean yield and probably improves seed quality. Similarly, rising oil and protein contents improves the soybean’s nutritional quality and will likely increase soybean yield. Due to the importance of these three seed traits in soybean breeding, extensive studies have been conducted on their underlying quantitative trait locus (QTLs) or genes and the dissection of their molecular regulatory pathways. This review summarized the progress in functional genome controlling soybean seed size, oil and protein contents in recent decades, and presented the challenges and prospects for developing high-yield soybean cultivars with high oil or protein content. In the end, we hope this review will be helpful to the improvement of soybean yield and quality in the future breeding process.

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“…For instance, 396 QTLs are associated with SW and SS, 333 with seed oil content, and 234 with seed protein content. Some of these QTLs, including those relating to protein content, oil accumulation, and seed size, had overlapping areas, indicating the presence of pleiotropic regulating genes in these QTLs ( Wang et al., 2015a ; Cui et al., 2020 ; Kumawat and Xu, 2021 ; Kumar et al., 2022 ; Luo et al., 2022 ). Additionally, characteristics like SS, SW, NPP, number of seeds per pod, and HSW are key component traits directly influencing crop yield.…”

Section: Key Seed Yield Traits and Significance For Crop Improvementmentioning

confidence: 99%

“…For example, 19 QTLs were identified for HSW in individual and combined environments, among which seven novel minor ( R 2 < 10%), 2 ( qSW-17-1 and qSW-17-4) major ( R 2 > 10%), and eight stable QTLs ( Karikari et al., 2019 ). Recently, 3 major QTLs ( q100SW-4-1, q100SW-11-1 , and q100SW-17-1 ) with PVEs of 11.41%, 14.67%, and 14.37%, respectively, were identified ( Kumar et al., 2023 ).…”

Section: Molecular Genetic and Genomics Basis Of Soybean Yield Traitsmentioning

confidence: 99%

Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean

Tayade,

Imran,

Ghimire

et al. 2023

Front. Plant Sci.

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Soybean (Glycine max L. Merr.) is a crucial oilseed cash crop grown worldwide and consumed as oil, protein, and food by humans and feed by animals. Comparatively, soybean seed yield is lower than cereal crops, such as maize, rice, and wheat, and the demand for soybean production does not keep up with the increasing consumption level. Therefore, increasing soybean yield per unit area is the most crucial breeding objective and is challenging for the scientific community. Moreover, yield and associated traits are extensively researched in cereal crops, but little is known about soybeans’ genetics, genomics, and molecular regulation of yield traits. Soybean seed yield is a complex quantitative trait governed by multiple genes. Understanding the genetic and molecular processes governing closely related attributes to seed yield is crucial to increasing soybean yield. Advances in sequencing technologies have made it possible to conduct functional genomic research to understand yield traits’ genetic and molecular underpinnings. Here, we provide an overview of recent progress in the genetic regulation of seed size in soybean, molecular, genetics, and genomic bases of yield, and related key seed yield traits. In addition, phytohormones, such as auxin, gibberellins, cytokinins, and abscisic acid, regulate seed size and yield. Hence, we also highlight the implications of these factors, challenges in soybean yield, and seed trait improvement. The information reviewed in this study will help expand the knowledge base and may provide the way forward for developing high-yielding soybean cultivars for future food demands.

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

Cited by 15 publications

References 59 publications

Construction of Genetic Map and QTL Mapping for Seed Size and Quality Traits in Soybean (Glycine max L.)

Construction of Genetic Map and QTL Mapping for Seed Size and Quality Traits in Soybean (Glycine max L.)

Genetic regulatory networks of soybean seed size, oil and protein contents

Molecular, genetic, and genomic basis of seed size and yield characteristics in soybean

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