DataSheet_1_Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen.docx

IntroductionOryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource.
MethodsA new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes.
Results and DiscussionMore than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding.

引言
高秆野生稻（Oryza alta Swallen）是异源四倍体多年生野生稻类群，携带有CCDD基因组，其基因组中可能蕴藏可用于丰富水稻遗传资源的优良基因。

方法
本实验室以高秆野生稻（Oryza alta Swallen）为材料，培育得到全新野生稻品系“华野5号”。本研究采用全基因组重测序与泛基因组分析技术，对该品系的基因组变异与新基因进行系统解析。

结果与讨论
与亚洲栽培稻参考基因组相比，本研究共检测到超过一千万个基因组变异位点。在变异基因中，分别有724个基因编码蛋白激酶、197个编码合成酶、710个编码转录因子。另有共计353个、131个和135个变异基因分别与形态性状、生理性状、抗逆或耐逆性状相关。本研究共检测到62个NBS-LRR类基因，其中11个在叶鞘与成熟茎秆中表达，26个在幼根与成熟根中表达。通过整合8份高秆野生稻（Oryza alta, OA）、2份大颖野生稻（Oryza grandiglumis, OG）以及18份阔叶野生稻（Oryza latifolia, OL）的种质材料，本研究构建了CCDD基因组型野生稻物种的泛基因组序列。研究共发现28个非参考基因组NBS-LRR类基因，其中7个主要在成熟根中表达。本研究证实高秆野生稻（Oryza alta Swallen）蕴含丰富的DNA遗传变异，可为水稻抗逆育种提供全新的种质资源。