Katie O'Connor1,2, Ben Hayes3, Craig Hardner3, Catherine Nock4, Abdul Baten4,5, Mobashwer Alam3, Robert Henry3, Bruce Topp3. 1. Queensland Department of Agriculture and Fisheries, Maroochy Research Facility, Nambour, Qld, Australia. katie.oconnor@daf.qld.gov.au. 2. Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, Australia. katie.oconnor@daf.qld.gov.au. 3. Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Qld, Australia. 4. Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia. 5. AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.
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 4113 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.
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 4113 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.
Authors: Mohamed Cassim Mohamed Zakeel; Mobashwer Alam; Andrew D W Geering; Bruce Topp; Olufemi A Akinsanmi Journal: Front Plant Sci Date: 2021-12-24 Impact factor: 5.753
Authors: S Sheoran; S Jaiswal; N Raghav; R Sharma; A Gaur; J Jaisri; Gitanjali Tandon; S Singh; P Sharma; R Singh; M A Iquebal; U B Angadi; A Gupta; G Singh; G P Singh; A Rai; D Kumar; R Tiwari Journal: Front Plant Sci Date: 2022-02-11 Impact factor: 5.753