Parada-Rojas C H, Childs K L, Fernandez de Soto M, Salcedo A, Pecota K, Yencho G C, Almeyda C, Hamilton J P, Kitavi M, Buell C R, Conant G C, Baltzegar D, Quesada-Ocampo L M
North Carolina State University at Raleigh, Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, Raleigh, North Carolina, United States;
Michigan State University, Plant Biology Department, 612 Wilson Rd, Room 166, East Lansing, Michigan, United States, 48824;
Mol Plant Microbe Interact. 2025 Jul 12. doi: 10.1094/MPMI-03-25-0034-R.
Breeding for sweetpotato () resistance requires accelerating our understanding of genomic sources of resistance. Nucleotide-binding domain leucine-rich repeat receptors (NLRs) proteins represent a key component of the plant immune system that mediate plant immune responses. We cataloged the NLR diversity in 32 hexaploid sweetpotato genotypes and three diploid wild relatives using resistance gene enrichment sequencing (RenSeq) to capture and sequence full NLRs. A custom designed NLR bait-library enriched NLR genes with an average 97% target capture rate. We employed a curated database of cloned and functionally characterized NLRs to assign sequenced sweetpotato NLRs to canonical phylogenetic clades. We identified between 800 to 1,200 complete NLRs, highlighting the expanded diversity of coiled-coil NLRs (CNLs) across all genotypes. NLRs among sweetpotato genotypes exhibited large conservation across genotypes. Phylogenetic distance between 6X (hexaploid) and 2X (diploid) genotypes revealed that a small repertoire of CNLs diverged from the sweetpotato wild relatives. Finally, we obtained chromosome coordinates in hexaploid (Beauregard) and diploid () genomes and recorded clustering of NLRs on chromosomes arms. Our study provides a catalog of NLR genes that can be used to accelerate breeding and increase our understanding of evolutionary dynamics of sweetpotato NLRs.
培育抗甘薯（）品种需要加快我们对抗性基因组来源的理解。核苷酸结合域富含亮氨酸重复序列受体（NLRs）蛋白是植物免疫系统的关键组成部分，介导植物免疫反应。我们利用抗性基因富集测序（RenSeq）对32个六倍体甘薯基因型和3个二倍体野生近缘种的NLR多样性进行了编目，以捕获并测序完整的NLRs。一个定制设计的NLR诱饵文库富集了NLR基因，平均目标捕获率为97%。我们使用了一个经过整理的已克隆且具有功能特征的NLRs数据库，将测序得到的甘薯NLRs归入典型的系统发育分支。我们鉴定出800至1200个完整的NLRs，突出了所有基因型中卷曲螺旋NLRs（CNLs）的多样性扩展。甘薯基因型之间的NLRs在基因型间表现出很大的保守性。六倍体（六倍体）和二倍体（）基因型之间的系统发育距离表明，一小部分CNLs与甘薯野生近缘种不同。最后，我们在六倍体（Beauregard）和二倍体（）基因组中获得了染色体坐标，并记录了NLRs在染色体臂上的聚类情况。我们的研究提供了一个NLR基因目录，可用于加速育种并增进我们对甘薯NLRs进化动态学的理解。
