Nucleotide diversity and linkage disequilibrium in five Lolium perenne genes with putative role in shoot morphology

Knowledge on nucleotide diversity and linkage disequilibrium (LD) patterns is prerequisite for association analyses. However, little is known about the nucleotide diversity in the evolutionary important ryegrass shoot morphology genes. Five candidate genes, LpIAA1, LpRUB1, LpBRI1, LpSHOOT1 and LpTB1, with putative function on shoot morphology were studied in a panel of 20 diploid heterozygous ryegrass genotypes. The total length of alignments was 5120 bp or slightly more than 1 kb per gene. A total of 213 single nucleotide polymorphisms (SNPs) and 41 insertions/deletions (Indels) were detected. On average, one SNP was present every 94 bp between two randomly selected sequences for the five genes. As expected, the number of synonymous substitutions was much higher compared to the number of non-synonymous mutations for most of the genes. However, six non-synonymous and only two synonymous substitutions were detected in LpTB1. A negative and significant (P < 0.05) Tajima's D value was detected in the coding region of LpBRI1, suggesting selection and presence of low-frequency alleles for this gene. The number of haplotypes within the 5 genes across the 20 heterozygous genotypes ranged from 9 in LpIAA1 to 16 in both LpRUB1 and LpTB1, with an average of 14 alleles per gene. Low intragenic linkage disequilibrium (LD) (average r2 = 0.21–0.26) was observed for three genes, LpIAA1, LpRUB1 and LpSHOOT1, while LpTB1 and LpBRI1 showed substantially higher average LD levels of r2 = 0.56 and r2 = 0.59, respectively. No evidence of selection was found for LpIAA1, LpRUB1, LpSHOOT1 and LpTB1 genes, however, a significant and negative Tajima's D as well as high average LD in LpBRI1 suggest a role of this gene in shaping ryegrass shoot morphology during development of elite germplasm.