Resequencing of white jute (Corchorus capsularis L.) provides insights into genome diversity, population historical dynamics, and improvement

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Jute is an important natural fibre crop which provides most of the global bast fibre production annually. However, little progress has been made regarding its genomic diversity, historical population dynamics, origins, and improvement. In this study, we re-sequenced 150 accessions of white jute from 9 countries, further studied the genetic diversity, population dynamics, and improvement, and obtained a total of 3269,808 single nucleotide polymorphisms(SNPs) and 1179,601 insertions/deletions(InDels). Based on these markers, 150 accessions were classified into 2 clades: landraces and modern cultivars. Notably, the modern cultivars were partly classified into two offspring groups: one group developed from “D154,” an important Indian variety, and another from “Xin Xuan 1 hao,” a Chinese cultivar. The genetic diversity (π) was estimated for landrace and cultivars at 0.334 × 10−3 and 0.279 × 10−3, which was considerably lower than that for Corchorus olitorius, suggesting that C. capsularis is subject to a stronger breeding selection during improvement than C. olitorius. A total of 12 candidate genes related to improvement were identified by analyzing π and fixation index(FST). Three of the 12 genes may be involved in the methylation and demethylation processes, which can be integrated into an environmentally sensitive molecular engine that promotes rapid improvement. Analysis of population historical dynamics for C. capsularis showed that the population sizes for landraces and modern cultivars went through 3 bottlenecks. The first bottleneck may be due to climate change whereas the last two may be affected by human activities and war. Our results provide new insights into C. capsularis genome variation, phylogenetic relationships, and improvement, helping understand the genetic basis of crucial agronomic traits and facilitating future molecular breeding for jute.