AUTHOR=Shivute Fimanekeni Ndaitavela , Zhong Yi , Wu Jinwen , Bao Yueming , Wang Wei , Liu Xiangdong , Lu Zijun , Yu Hang 

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

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1345708

DOI=10.3389/fpls.2024.1345708

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p><italic>Oryza alta</italic> Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource.</p></sec><sec><title>Methods</title><p>A new wild rice line, Huaye 5, was developed from <italic>Oryza alta</italic> Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes.</p></sec><sec><title>Results and Discussion</title><p>More 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 <italic>Oryza alta</italic> (OA), 2 <italic>Oryza grandiglumis</italic> (OG) and 18 <italic>Oryza latifolia</italic> (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 <italic>Oryza alta</italic> Swallen that may provide a new germplasm for rice resistance breeding.</p></sec>