Genome-wide association studies for yield component traits in a macadamia breeding population

Abstract

Background: Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. 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. 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 4,113 SNPs. ASReml-R was used to perform association analyses with linear mixed models including a genomic relationship matrix to account for population structure. 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. Results: Seven SNPs were significantly associated with NW (at a genome-wide false discovery rate of <0.05), and four with WK. Multiple regression, as well as mapping of markers to genome assembly scaffolds suggested that some SNPs were detecting the same QTL. There were 44 significant SNPs identified for TC although multiple regression suggested detection of 16 separate QTLs. Conclusions: These findings have important implications for macadamia breeding, and highlight the difficulties of heterozygous populations with rapid LD decay. By coupling validated marker-trait associations detected through GWAS with MAS, genetic gain could be increased by reducing the selection time for economically important nut characteristics. Genomic selection may be a more appropriate method to predict complex traits like tree size and yield.

Genomic selection and genetic gain for nut yield in an Australian macadamia breeding population

“…Future work employing GS to increase genetic gain in macadamia could investigate other economically important traits, such as tree size. In the same population as the current study, O'Connor et al [18] found 16 QTLs linked with trunk circumference. The large number of markers associated with this trait, compared with other traits in the study, means that GS may be more appropriate than GWAS and MAS to increase genetic gain, given the seemingly quantitative nature of trunk circumference.…”

“…MAS can also be conducted using genetic markers of large effect detected through genome-wide association studies (GWAS). GWAS has been conducted in macadamia for nut and kernel traits, but not for yield [17,18].…”

Genome-Wide Association Study and Post-genome-Wide Association Study Analysis for Spike Fertility and Yield Related Traits in Bread Wheat

“…The future genetic gain is more likely from a genomics-driven breeding program which requires an in-depth understanding of all the major/minor quantitative trait loci (QTLs) segregating in the elite germplasm pools. GWAS has been found a powerful tool for dissecting complex traits by finding causative allelic variation at individual SNP markers or associated with natural phenotypic variation (Alqudah et al, 2020) which can be used effectively to fine map these traits (Garcia et al, 2019;Sheoran et al, 2019;Alqudah et al, 2020;Kumar et al, 2020;O'Connor et al, 2020;Sehgal et al, 2020). This approach has been widely used to predict phenotypically related candidate genes in many crops (Si et al, 2016;Wang et al, 2016;Liu et al, 2018).…”

An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome

“…Despite its size (>1,660 species; Christenhusz & Byng, 2016), the Proteaceae has received minimal attention from genome researchers, probably due to most diversity being restricted to the southern hemisphere as well as the nut‐producing macadamia tree being the only species within this family of significant worldwide economic interest. A genome assembly of Macadamia integrifolia has been developed (Nock et al, 2020), the information from which is used for genome‐informed breeding (O’Connor et al, 2020). Very little genetic information is available for K. exselsa ; however, karyotype analysis indicated it is a diploid species with n = 14 chromosomes (Hair & Beuzenberg, 1958).…”