Overview of the Australian macadamia industry breeding program

Topp, Bruce; Hardner, Craig; Neal, Jodi; Kelly, A.; Russell, D.; McConchie, C. A.; O'Hare, P.

doi:10.17660/actahortic.2016.1127.8

Cited by 23 publications

(30 citation statements)

References 10 publications

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“…The Australian macadamia breeding program's B1.2 population is the focus of this study. The entire population included 2000 seedlings from 141 families, which were planted across nine locations in southeast Queensland and northeast New South Wales, Australia, between 2001and 2003(Topp et al, 2016. This study involved 281 progeny from 32 families across four of these sites in Queensland, as well as 18 of their 29 parents (n = 299).…”

Section: Methodsmentioning

confidence: 99%

Selecting for Nut Characteristics in Macadamia Using a Genome-wide Association Study

O’Connor¹,

Hayes²,

Hardner³

et al. 2019

horts

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Additional index words. GWAS, nut weight, kernel weight, kernel recovery, SNP markers, breeding Abstract. Current macadamia breeding programs involve a lengthy and laborious twostage selection process: evaluation of a large number of unreplicated seedling progeny, followed by replicated trials of clonally propagated elite seedlings. Yield component traits, such as nut-in-shell weight (NW), kernel weight (KW), and kernel recovery (KR) are commercially important, are more easily measured than yield, and have a higher heritability. A genome-wide association study (GWAS) combined with marker-assisted selection offers an opportunity to reduce the time of candidate evaluation. In this study, a total of 281 progeny from 32 families, and 18 of their 29 parents have been genotyped for 7126 single nucleotide polymorphism (SNP) markers. A GWAS was performed using ASReml with 4352 SNPs. We found five SNPs significantly associated with NW, nine with KW, and one with KR. Further, three of the top 10 markers for NW and KW were shared between the two traits. Future macadamia breeding could involve prescreening of individuals for desired traits using these significantly associated markers, with only predicted elite individuals continuing to the second stage of selection, thus potentially reducing the selection process by 7 years.

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Section: Methodsmentioning

confidence: 99%

Selecting for Nut Characteristics in Macadamia Using a Genome-wide Association Study

O’Connor¹,

Hayes²,

Hardner³

et al. 2019

horts

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“…Reduced tree size is also an important selection trait to increase planting density and subsequent yield per hectare (29,30). Trunk circumference (TC) or trunk cross-sectional area can be used as an estimate of tree size in macadamia (30).…”

Section: Introductionmentioning

confidence: 99%

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

O’Connor

Hayes

Hardner

et al. 2019

Preprint

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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.

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“…The need for an industry-supported breeding program to develop new cultivars adapted specifically to the Australian production environments was identified in the early 1990s (Hardner and McConchie, 1999;Stephenson, 1990b;Winks, 1983). The Australian macadamia breeding program adopted a quantitative genetic-focused approach that employed improved experimental design, structured populations to support analysis with quantitative genetic-based linear mixed models, and selection index to identify candidates with the greatest likelihood of delivering improved profits to the Australian industry (Hardner and McConchie, 1999;Hardner and Peace, 2010;Mehlenbacher, 2003;Topp et al, 2016). The breeding strategy comprised two phases: 1) evaluation of recombinant seedling progeny to identify candidate cultivars for further testing; and 2) evaluation of candidate cultivars in clonal regional variety trials to identify cultivars for release.…”

mentioning

confidence: 99%