Seven SNPs were significantly associated with NW (at a genome-wide false discovery rate of < 0.05), and four with WK. Traits investigated were: nut weight (NW), kernel weight (KW), kernel recovery (KR), percentage of whole kernels (WK), tree trunk circumference (TC), percentage of racemes that survived from flowering through to nut set, and number of nuts per raceme. ASReml-R was used to perform association analyses with linear mixed models including a genomic relationship matrix to account for population structure. This study used 295 progeny from 32 full-sib families and 29 parents (18 phenotyped) which were planted across four sites, with each tree genotyped for 4113 SNPs. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost.
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