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

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

doi:10.3389/fpls.2024.1345708

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

Front Plant Sci. 2024 Apr 8:15:1345708. doi: 10.3389/fpls.2024.1345708. eCollection 2024.

Authors

Fimanekeni Ndaitavela Shivute^#^{1

2

3}, Yi Zhong^#^{1

2

3}, Jinwen Wu^{1

2

3}, Yueming Bao^{1

2

3}, Wei Wang^{1

2

3}, Xiangdong Liu^{1

2

3}, Zijun Lu^{1

2

3}, Hang Yu⁴

Affiliations

¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China.
² Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China.
³ College of Agriculture, South China Agricultural University, Guangzhou, China.
⁴ Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.

^# Contributed equally.

Abstract

Introduction: Oryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource.

Methods: A 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 discussion: 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 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.

Keywords: Oryza alta swallen; genome sequencing; germplasm; pan-genome; wild rice.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by National Key R&D Program of China (2023YFD1200802), the Base Bank of Lingnan Rice Germplasm Resources Project (2023-40), Project funded by China Postdoctoral Science Foundation (2022M721212), the Laboratory of Lingnan Modern Agriculture Project (NT2021001), the Natural Science Foundation of Guangdong Province (2022A1515011741), and Special Funds for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science (R2021YJYB3017).