Low-call-rate SNPs and presence-absence variation identified in the rice pan-genome can improve genomic prediction of rice gene bank accessions.

ABSTRACT:

Key message

Substantial improvements in genomic prediction accuracy for rice gene bank accessions were achieved by incorporating SNPs of low call rate identified in a recently published rice pan-genome. Introduction of useful genetic variation to breeding populations is a key factor in achieving genetic gain in crop breeding. However, identifying donors from genetic diversity stored in gene banks requires extensive phenotyping, which is not feasible for many traits of interest. Genomic prediction (GP) of phenotypic values has been proposed to overcome this phenotyping bottleneck. A key challenge for GP is the identification of appropriate markers representative of genetic variation causal for phenotypes. Here we report on utilizing single nucleotide polymorphisms (SNPs) from the co

SUBMITTER: Krusenbaum L 

PROVIDER: S-EPMC12594682 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature