Abstract
Seed size and shape are important traits determining yield and quality in soybean. However, the genetic mechanism and genes underlying these traits remain largely unexplored. In this regard, this study used two related recombinant inbred line (RIL) populations (ZY and K3N) evaluated in multiple environments to identify main and epistatic-effect quantitative trait loci (QTLs) for six seed size and shape traits in soybean. A total of 88 and 48 QTLs were detected through composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively, and 15 QTLs were common among both methods; two of them were major (R2 > 10%) and novel QTLs (viz., qSW-1-1ZN and qSLT-20-1K3N). Additionally, 51 and 27 QTLs were identified for the first time through CIM and MCIM methods, respectively. Colocalization of QTLs occurred in four major QTL hotspots/clusters, viz., “QTL Hotspot A”, “QTL Hotspot B”, “QTL Hotspot C”, and “QTL Hotspot D” located on Chr06, Chr10, Chr13, and Chr20, respectively. Based on gene annotation, gene ontology (GO) enrichment, and RNA-Seq analysis, 23 genes within four “QTL Hotspots” were predicted as possible candidates, regulating soybean seed size and shape. Network analyses demonstrated that 15 QTLs showed significant additive x environment (AE) effects, and 16 pairs of QTLs showing epistatic effects were also detected. However, except three epistatic QTLs, viz., qSL-13-3ZY, qSL-13-4ZY, and qSW-13-4ZY, all the remaining QTLs depicted no main effects. Hence, the present study is a detailed and comprehensive investigation uncovering the genetic basis of seed size and shape in soybeans. The use of a high-density map identified new genomic regions providing valuable information and could be the primary target for further fine mapping, candidate gene identification, and marker-assisted breeding (MAB).
Highlights
Soybean (Glycine max L.) is one of the most economically important crops, being a rich source of both edible oil and protein, and can fix atmospheric nitrogen through a symbiotic association with microorganisms in the soil, and are used as a model plant for legume research [1]
All six traits related to seed size and shape showed different levels of distribution in both recombinant inbred line (RIL) populations (ZY and K3N), with mostly skewness and kurtosis 3%, which is typical for quantitative traits, indicating the suitability of these populations for Quantitative trait loci (QTL) mapping (Figure 1 and Table S1a,b)
88 and 48 QTLs were detected through composite interval mapping (CIM) and model-based composite interval mapping (MCIM), respectively, including 15 common QTLs, with two major (R2 > 10%) and novel QTLs, viz., qSW-1-1ZY and qSLT-20-1K3N
Summary
Soybean (Glycine max L.) is one of the most economically important crops, being a rich source of both edible oil and protein, and can fix atmospheric nitrogen through a symbiotic association with microorganisms in the soil, and are used as a model plant for legume research [1]. Yield-related traits are the key target of plant breeders to improve soybean yield/production In this regard, traits related to seed size and shape are the crucial parameters determining seed-weight and yield in soybean [3,4]. For the production of fermented soybeans (natto) and sprouts, small-seeded cultivars are suitable, while for soymilk, green soybeans (edamame), boiled soybeans (nimame), and soybean curd (tofu), large-seeded varieties are used [11,12,13] These traits influence the germination ability and seedling vigor, and that, in turn, plays an essential role in determining the competitive strength of the seedlings for light, nutrient resources, and stress tolerance [14,15,16]
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