Abstract
BackgroundAssociation analysis is an alternative way for QTL mapping in ryegrass. So far, knowledge on nucleotide diversity and linkage disequilibrium in ryegrass is lacking, which is essential for the efficiency of association analyses.Results11 expressed disease resistance candidate (R) genes including 6 nucleotide binding site and leucine rich repeat (NBS-LRR) like genes and 5 non-NBS-LRR genes were analyzed for nucleotide diversity. For each of the genes about 1 kb genomic fragments were isolated from 20 heterozygous genotypes in ryegrass. The number of haplotypes per gene ranged from 9 to 27. On average, one single nucleotide polymorphism (SNP) was present per 33 bp between two randomly sampled sequences for the 11 genes. NBS-LRR like gene fragments showed a high degree of nucleotide diversity, with one SNP every 22 bp between two randomly sampled sequences. NBS-LRR like gene fragments showed very high non-synonymous mutation rates, leading to altered amino acid sequences. Particularly LRR regions showed very high diversity with on average one SNP every 10 bp between two sequences. In contrast, non-NBS LRR resistance candidate genes showed a lower degree of nucleotide diversity, with one SNP every 112 bp. 78% of haplotypes occurred at low frequency (<5%) within the collection of 20 genotypes. Low intragenic LD was detected for most R genes, and rapid LD decay within 500 bp was detected.ConclusionSubstantial LD decay was found within a distance of 500 bp for most resistance candidate genes in this study. Hence, LD based association analysis is feasible and promising for QTL fine mapping of resistance traits in ryegrass.
Highlights
Association analysis is an alternative way for QTL mapping in ryegrass
The objectives of this study were to (1) identify single nucleotide polymorphism (SNP) for allele tracing in GRASP within about 1 kb fragments of expressed resistance candidate genes, (2) compare the nucleotide diversity within and between different resistance candidate genes, (3) determine the extent and structure of linkage disequilibrium (LD) within these genes, and (4) discuss the prospects of candidategene based association mapping in ryegrass
A total of 10,971 bp were aligned over all loci for the 20 genotypes, the length of sequence alignment for each gene was about 1 kb (904–1085 bp), which is used to develop markers for candidate gene allele tracing in selection experiments
Summary
Association analysis is an alternative way for QTL mapping in ryegrass. Major agronomic traits for this species such as forage quality are quantitatively inherited [1]. QTL mapping has been demonstrated as a successful method to dissect the genetic bases of complex traits in several important crops since the 1990s. Due to its self-incompatibility, populations of doubled haploid lines (DHs) or recombinant inbred lines (RILs) favorable for QTL mapping in other crops are difficult to develop in ryegrass. Association studies based on linkage disequilibrium (LD) mapping could be an alternative and more efficient way for QTL/gene tagging in ryegrass. The high degree of genetic variation between and within ryegrass populations might be beneficial for identification of both genes and polymorphisms affecting quantitative inherited characters for development of informative "functional markers" [6]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
