Abstract
Plants have developed sophisticated systems to adapt to local conditions during evolution, domestication and natural or artificial selection. The selective pressures of these different growing conditions have caused significant genomic divergence within species. The flowering time trait is the most crucial factor because it helps plants to maintain sustainable development. Controlling flowering at appropriate times can also prevent plants from suffering from adverse growth conditions, such as drought, winter hardness, and disease. Hence, discovering the genome-wide genetic mechanisms that influence flowering time variations and understanding their contributions to adaptation should be a central goal of plant genetics and genomics. A global core collection panel with 448 inbred rapeseed lines was first planted in four independent environments, and their flowering time traits were evaluated. We then performed a genome-wide association mapping of flowering times with a 60 K SNP array for this core collection. With quality control and filtration, 20,342 SNP markers were ultimately used for further analyses. In total, 312 SNPs showed marker-trait associations in all four environments, and they were based on a threshold p-value of 4.06 × 10−4; the 40 QTLs showed significant association with flowering time variations. To explore flowering time QTLs and genes related to growth habits in rapeseed, selection signals related to divergent habits were screened at the genome-wide level and 117 genomic regions were found. Comparing locations of flowering time QTLs and genes with these selection regions revealed that 20 flowering time QTLs and 224 flowering time genes overlapped with 24 and 81 selected regions, respectively. Based on this study, a number of marker-trait associations and candidate genes for flowering time variations in rapeseed were revealed. Moreover, we also showed that both flowering time QTLs and genes play important roles in rapeseed growth habits. These results will be applied to rapeseed breeding programs, and they will aid in our understanding of the relation between flowering time variations and growth habits in plants.
Highlights
Plants have developed sophisticated systems to adapt to local conditions over the long history of evolution, domestication and natural or artificial selection (Anderson et al, 2011)
We found that 7 of the 40 flowering QTLs in this study have been reported by studies on TN doubled haploid (DH) mapping population, 5 have been reported by studies performed on 158 European wintertype B. napus inbred lines (Schiessl et al, 2015) and 5 have been reported by studies performed on a diversity panel comprising 523 B. napus cultivars and inbred lines (Xu et al, 2016) (Table S2)
Given the limited information and different algorithms between linkage (QTL mapping) and linkage disequilibrium mapping (GWAS), we speculated that the numbers of QTLs reported by previous studies would be larger than 13
Summary
Plants have developed sophisticated systems to adapt to local conditions over the long history of evolution, domestication and natural or artificial selection (Anderson et al, 2011) These systems can be attributed to both physiological and genetic mechanisms, and they have resulted in divergent populations within a single species that grow in different geographic areas or different seasons. This finding further suggests that genomic regions have been targeted by selection and are expected to exhibit characteristic changes in their levels and/or patterns of nucleotide diversity within species. Understanding the genome-wide genetic architecture that controls variations in flowering time and growth habits would be a central goal in plant genetics and genomics
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