Open AccessA genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola
Author(s) -
Alkesh Hada,
Uma Rao,
Nisha Singh,
Balwant Singh,
Vandna Rai,
Nagendra Singh,
Uma Rao
Publication year - 2020
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0239085
Subject(s) - biology , oryza sativa , quantitative trait locus , single nucleotide polymorphism , wrky protein domain , oryza rufipogon , oryza , genetics , myb , population , candidate gene , gall , root knot nematode , gene , nematode , botany , genotype , transcriptome , gene expression , ecology , demography , sociology
Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice ( Oryza sativa ) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions ( O . nivara , O . rufipogon , O . sativa f. spontanea ) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs ( s ingle n ucleotide p olymorphism) genotyped by 50K “OsSNPnks” genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly ( P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.