Genome data from sweet and grain sorghum (Sorghum bicolor)

Sorghum is produced globally as a source of food, feed, fiber, and fuel. Grain and sweet sorghums differ in a number of important traits including stem sugar and juice accumulation, plant height, and the production of grain and biomass. The first sorghum whole-genome sequences are now available for analysis, but additional genomic sequences will be required to study genome-wide and intraspecific variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C4 crop. In a joint effort with scientists from the Institute of Botany of Chinese Academy of Sciences (Beijing) and Temasek Life Sciences Laboratory (Singapore), BGI resequenced two sweet and one grain sorghum inbred lines: E-Tian, Ji2731, and Keller. E-Tian (literally meaning Russian Sweet in Chinese) is a sweet sorghum line introduced into China in the early 1970’s. Ji2731 is a Chinese kaoliang grain sorghum that is well adapted to Northeast China. Keller is an American-bred elite sweet sorghum line shown to perform well across a wide range of environmental conditions. Using the re-sequencing data, a set of nearly 1,500 genes differentiating sweet and grain sorghum were identified. These genes fall into 10 major metabolic pathways involved in sugar and starch metabolisms, lignin and coumarin biosynthesis, nucleic acid metabolism, stress responses and DNA damage repair. In addition, 1,057,018 SNPs, 99,948 indels of 1-10bp in length and 16,487 presence/absence variations were uncovered, and 17,111 CNVs were detected. The majority of the SNPs, large-effect SNPs, indels and presence/absence variations resided in genes containing leucine rich repeats, PPR repeats and disease resistance R genes possessing diverse biological functions or under diversifying selection, but were absent in genes which are essential for life. This is the first publically available data that allows the identification of genome-wide patterns of genetic variation in sorghum. The high-density SNP and indel markers presented here will be a valuable resource for future genotype and phenotype studies and the molecular breeding of this important crop and for related species.

高粱（Sorghum）是全球范围内广泛种植的粮用、饲用、纤维及能源作物。粒用高粱与甜高粱在多项重要性状上存在显著差异，包括茎秆糖分与汁液积累量、株高，以及籽粒和生物量的生产能力。目前首个高粱全基因组序列已公开可供分析，但要解析这类重要性状的遗传基础，并对这一关键C4作物开展定制化育种，仍需获取更多基因组序列以开展全基因组水平及种内变异研究。本研究与中国科学院植物研究所（北京）、淡马锡生命科学实验室（新加坡）的科研团队合作，由华大基因（BGI）对2份甜高粱自交系与1份粒用高粱自交系进行了重测序，对应的品系分别为E-Tian、Ji2731与Keller。其中，E-Tian（中文字面含义为“俄罗斯甜”）是20世纪70年代初引入我国的甜高粱品系；Ji2731是适配我国东北地区种植的中国高粱（kaoliang）粒用品种；Keller则是美国选育的优良甜高粱品系，在多种环境条件下均表现出优异的生长性状。基于本次重测序数据，研究团队共鉴定出近1500个可区分甜高粱与粒用高粱的差异基因，这些基因隶属于10条主要代谢通路，涵盖糖与淀粉代谢、木质素及香豆素生物合成、核酸代谢、胁迫响应以及DNA损伤修复。此外，本研究共检出1057018个单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）、99948个长度为1-10bp的插入缺失变异（insertion-deletion, indels）、16487个存在/缺失变异（presence/absence variations, PAVs），以及17111个拷贝数变异（Copy Number Variation, CNVs）。多数SNPs、大效应SNPs、插入缺失变异及存在/缺失变异富集于富含亮氨酸重复序列、PPR重复序列及抗病R基因的基因家族中，这类基因往往具有多样的生物学功能或处于多样化选择压力之下，而在生命必需基因中则鲜有这类变异的分布。本研究是首个公开可用于解析高粱全基因组遗传变异模式的数据资源。本次发布的高密度SNP与indel标记，将为该作物及其近缘物种的后续基因型-表型关联研究、分子育种工作提供极具价值的研究工具与数据基础。