Abstract
Understanding the genetic mechanism underlying seed size, shape, and weight is essential for enhancing soybean cultivars. High-density genetic maps of two recombinant inbred line (RIL) populations, LM6 and ZM6, were evaluated across multiple environments to identify and validate M-QTLs as well as identify candidate genes behind major and stable quantitative trait loci (QTLs). A total of 239 and 43 M-QTLs were mapped by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM) approaches, from which 180 and 18, respectively, are novel QTLs. Twenty-two QTLs including four novel major QTLs were validated in the two RIL populations across multiple environments. Moreover, 18 QTLs showed significant AE effects, and 40 pairwise of the identified QTLs exhibited digenic epistatic effects. Thirty-four QTLs associated with seed flatness index (FI) were identified and reported here for the first time. Seven QTL clusters comprising several QTLs for seed size, shape, and weight on genomic regions of chromosomes 3, 4, 5, 7, 9, 17, and 19 were identified. Gene annotations, gene ontology (GO) enrichment, and RNA-seq analyses of the genomic regions of those seven QTL clusters identified 47 candidate genes for seed-related traits. These genes are highly expressed in seed-related tissues and nodules, which might be deemed as potential candidate genes regulating the seed size, weight, and shape traits in soybean. This study provides detailed information on the genetic basis of the studied traits and candidate genes that could be efficiently implemented by soybean breeders for fine mapping and gene cloning, and for marker-assisted selection (MAS) targeted at improving these traits individually or concurrently.
Highlights
IntroductionMerr.) is one of the most important food crops, being a rich source of dietary protein (69%) and providing over 50% edible oil globally, and has a significant role in health and biofuel (Hoeck et al, 2003)
The present study has implemented high-density genetic maps constructed from two-related recombinant inbred line (RIL) populations LM6 and ZM6 comprising 2,267 and 2,601 bin markers, respectively (Li et al, 2017), to validate QTLs associated with seed size, shape, and weight
Mapping of QTLs associated with seed size, shape, and weight-related traits using the model-based composite interval mapping (MCIM) approach was performed to (i) dissect the additive effect QTLs and Q × E interactions, which is essential for selecting the most compatible varieties adapted to particular environments, and (ii) further validate the QTLs identified by the composite interval mapping (CIM) approach
Summary
Merr.) is one of the most important food crops, being a rich source of dietary protein (69%) and providing over 50% edible oil globally, and has a significant role in health and biofuel (Hoeck et al, 2003). Besides improving soil fertility by integrating atmospheric nitrogen in the soil through a synergistic interaction with microorganisms, because of its high nutritional value, soybean is used in human food and animal feed (Wang et al, 2019). Throughout the last five decades, soybean production in China slightly increased. China imports almost 80% of its requirements of soybean; improving soybean production is a major aim of soybean breeders to make the country self-sufficient (Liu et al, 2018). Most plant breeders are targeting yield-related traits to improve soybean production
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