Chengcheng Shi

Abstract Pearl millet [ Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D 2 B 1 -P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

Summary Allotetraploid oilseed rape ( Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B . napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi‐winter oilseed rape cultivar ‘ ZS 11’ and its comprehensive genomic comparison with the genomes of the winter‐type cultivar ‘Darmor‐ bzh ’ as well as two progenitors. The integrated BAC ‐to‐ BAC and whole‐genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high‐quality genome assembly of B . napus ‘ ZS 11’. Within a short evolutionary period (~6700 years ago), semi‐winter‐type ‘ ZS 11’ and the winter‐type ‘Darmor‐ bzh ’ maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to ‘Darmor‐ bzh ’, both two subgenomes of ‘ ZS 11’ are closely related to its progenitors, and the ‘ ZS 11’ genome harbored several specific segmental homoeologous exchanges ( HE s). Furthermore, the semi‐winter‐type ‘ ZS 11’ underwent potential genomic introgressions with B . rapa (A r ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03. FLC 3 regulating vernalization‐responsive flowering time in ‘ ZS 11’ was first experienced HE , and then underwent genomic introgression event with A r , which potentially has led to genetic differences in controlling vernalization in the semi‐winter types. Our observations improved our understanding of the genetic diversity of different B . napus morphotypes and the cultivation history of semi‐winter oilseed rape in Asia.