A Reference-Quality NLRome for the Hexaploid Sweetpotato and Diploid Wild Relatives.

IF 3.4 3区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular Plant-microbe Interactions Pub Date : 2025-07-12 DOI:10.1094/MPMI-03-25-0034-R

C H Parada-Rojas, K L Childs, M Fernandez de Soto, A Salcedo, K Pecota, G C Yencho, C Almeyda, J P Hamilton, M Kitavi, C R Buell, G C Conant, D Baltzegar, L M Quesada-Ocampo

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引用次数: 0

Abstract

Breeding for sweetpotato (Ipomea batatas) 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 I. batatas CNLs diverged from the sweetpotato wild relatives. Finally, we obtained chromosome coordinates in hexaploid (Beauregard) and diploid (Ipomoea trifida) 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.

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六倍体甘薯和二倍体野生近缘NLRome的参考品质。

甘薯（ipoma batatas）抗性育种需要加快我们对抗性基因组来源的理解。核苷酸结合域富亮氨酸重复受体（NLRs）蛋白是介导植物免疫应答的植物免疫系统的关键组成部分。利用抗性基因富集测序技术（RenSeq）对32个六倍体甘薯基因型和3个二倍体野生近缘进行NLR多样性分类。定制设计的NLR诱饵库富集NLR基因，平均靶捕获率为97%。我们利用一个精心整理的克隆和功能特征的nlr数据库，将测序的甘薯nlr分配到典型的系统发育进化枝。我们确定了800至1200个完整的nlr，突出了所有基因型中卷曲nlr （cnl）的扩大多样性。甘薯NLRs在不同基因型间表现出较大的保守性。6X（六倍体）和2X（二倍体）基因型之间的系统发育距离表明，一小部分甘薯cnl与甘薯野生近缘有分化。最后，我们获得了六倍体（Beauregard）和二倍体（Ipomoea trifida）基因组的染色体坐标，并记录了NLRs在染色体臂上的聚类。我们的研究提供了一个NLR基因目录，可以用来加速育种和增加我们对甘薯NLR进化动力学的理解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Molecular Plant-microbe Interactions 生物-生化与分子生物学

CiteScore

7.00

自引率

2.90%

发文量

250

审稿时长

3 months

期刊介绍： Molecular Plant-Microbe Interactions® (MPMI) publishes fundamental and advanced applied research on the genetics, genomics, molecular biology, biochemistry, and biophysics of pathological, symbiotic, and associative interactions of microbes, insects, nematodes, or parasitic plants with plants.