Fine mapping and identification of candidate genes for a QTL affecting Meloidogyne incognita reproduction in Upland cotton

BMC Genomics

Research Article

Robert L. Nichols¹  Rippy Singh²  Pawan Kumar²  Peng W. Chee²  Xinlian Shen³  Yajun He⁴  Daniel G. Peterson⁵  Andrew H. Paterson⁶  Hui Guo⁶  Richard F. Davis⁷ 

[1] Cotton Incorporated, 6399 Weston Parkway, 27513, Cary, NC, USA;Cotton Molecular Breeding Laboratory, University of Georgia, 31793, Tifton, GA, USA;Cotton Molecular Breeding Laboratory, University of Georgia, 31793, Tifton, GA, USA;Present Address: Biotechnology Institute, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, China;Cotton Molecular Breeding Laboratory, University of Georgia, 31793, Tifton, GA, USA;Present Address: College of Agronomy and Biotechnology, Southwest University, 400716, Chongqing, China;Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, 39762, Mississippi State, MS, USA;Plant Genome Mapping Laboratory, University of Georgia, 30602, Athens, GA, USA;USDA-ARS, Crop Protection and Management Research Unit, 31793, Tifton, GA, USA;

关键词: Cotton;    Root Knot Nematodes;    RKN;    QTLs;    SNP;    Candidate genes;   

DOI  :  10.1186/s12864-016-2954-1

 received in 2015-12-17, accepted in 2016-07-19,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe southern root-knot nematode (Meloidogyne incognita; RKN) is one of the most important economic pests of Upland cotton (Gossypium hirsutum L.). Host plant resistance, the ability of a plant to suppress nematode reproduction, is the most economical, practical, and environmentally sound method to provide protection against this subterranean pest. The resistant line Auburn 623RNR and a number of elite breeding lines derived from it remain the most important source of root-knot nematode (RKN) resistance. Prior genetic analysis has identified two epistatically interacting RKN resistance QTLs, qMi-C11 and qMi-C14, affecting gall formation and RKN reproduction, respectively.ResultsWe developed a genetic population segregating only for the qMi-C14 locus and evaluated the genetic effects of this QTL on RKN resistance in the absence of the qMi-C11 locus. The qMi-C14 locus had a LOD score of 12 and accounted for 24.5 % of total phenotypic variation for egg production. In addition to not being significantly associated with gall formation, this locus had a lower main effect on RKN reproduction than found in our previous study, which lends further support to evidence of epistasis with qMi-C11 in imparting RKN resistance in the Auburn 623RNR source. The locus qMi-C14 was fine-mapped with the addition of 16 newly developed markers. By using the reference genome sequence of G. raimondii, we identified 20 candidate genes encoding disease resistance protein homologs in the newly defined 2.3 Mb region flanked by two SSR markers. Resequencing of an RKN resistant and susceptible G. hirsutum germplasm revealed non-synonymous mutations in only four of the coding regions of candidate genes, and these four genes are consequently of high interest.ConclusionsOur mapping results validated the effects of the qMi-C14 resistance locus, delimiting the QTL to a smaller region, and identified tightly linked SSR markers to improve the efficiency of marker-assisted selection. The candidate genes identified warrant functional studies that will help in identifying and characterizing the actual qMi-C14 defense gene(s) against root-knot nematodes.

【 授权许可】

CC BY   
© The Author(s). 2016