Acceleration of Forest and Fruit Tree Domestication by Genomic Selection

Isik, Fikret; Kumar, Satish; Martínez-García, Pedro J.; Iwata, Hiroyoshi; Yamamoto, Takatsugu

doi:10.1016/bs.abr.2015.05.002

Cited by 26 publications

(19 citation statements)

References 99 publications

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“…The development of new tree fruit cultivars is an expensive and time‐consuming endeavor, but it is believed that new genomic technologies will help with its advancement by elucidating the genetic basis of commercially important traits and enabling MAS (Isik et al, 2015; Edge‐Garza et al, 2015). Arguably the most crucial steps toward establishing robust genotype‐phenotype associations that lead to MAS are the design of mapping populations and the collection of high‐quality phenotypic data (Ogura and Busch, 2015).…”

Section: Discussionmentioning

confidence: 99%

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A Genome‐Wide Association Study of Apple Quality and Scab Resistance

McClure¹,

Gardner

Douglas³

et al. 2018

The Plant Genome

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The apple (Malus × domestica Borkh.) is an economically and culturally important crop grown worldwide. Growers of this long-lived perennial must produce fruit of adequate quality while also combatting abiotic and biotic stress. Traditional apple breeding can take up to 20 yr from initial cross to commercial release, but genomics-assisted breeding can help accelerate this process. To advance genomics-assisted breeding in apple, we performed genome-wide association studies (GWAS) and genomic prediction in a collection of 172 apple accessions by linking over 55,000 single nucleotide polymorphisms (SNPs) with 10 phenotypes collected over 2 yr. Genomewide association studies revealed several known loci for skin color, harvest date and firmness at harvest. Several significant GWAS associations were detected for resistance to a major fungal pathogen, apple scab (Venturia ineaqualis [Cke.] Wint.), but we demonstrate that these hits likely represent a single ancestral source. Using genomic prediction, we show that most phenotypes are sufficiently predictable using genome-wide SNPs to be candidates for genomic selection. Finally, we detect a signal for firmness retention after storage on chromosome 10 and show that it may not stem from variation in PG1, a gene repeatedly identified in bi-parental mapping studies and widely believed to underlie a major QTL for firmness on chromosome 10. We provide evidence that this major QTL is more likely due to variation in a neighboring ethylene response factor (ERF) gene. The present study showcases the superior mapping resolution of GWAS compared to bi-parental linkage mapping by identifying a novel candidate gene underlying a well-studied, major QTL involved in apple firmness.

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Section: Discussionmentioning

confidence: 99%

“…One of the main advantages of GBS compared to SNP arrays is that one is not limited by a fixed set of SNPs when genotyping (Chagné, 2015). Another advantage is that the cost per data point for genotyping and whole genome sequencing continues to decline (Isik et al, 2015).…”

mentioning

confidence: 99%

A Genome‐Wide Association Study of Apple Quality and Scab Resistance

McClure¹,

Gardner

Douglas³

et al. 2018

The Plant Genome

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“…As for standard marker-assisted selection, the primary limitation in applying genomic selection to new and orphan crops is the absence of phenotypic data from relevant training populations (Varshney et al, 2012). However, application of the approach could in theory be especially effective for slowmaturing perennial new and orphan crops which are difficult to directly phenotype for key production traits (Isik et al, 2015). Genomic selection may also be particularly effective when the underlying biological basis of key traits is poorly understood, as is the case with many new and orphan crops.…”

Section: Fruit Sizementioning

confidence: 99%

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

et al. 2019

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Summary Especially in low‐income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low‐input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, namely: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop ‘rewildings’.

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“…Screening seedlings for markers significantly associated with important traits could predict these trait measurements years before they are actually expressed. As such, GWAS followed by MAS is a feasible way of accelerating selection cycles, by selecting candidate cultivars at an earlier stage, and thus improving genetic gain (Khan and Korban, 2012;Isik et al, 2015).…”

mentioning

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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Acceleration of Forest and Fruit Tree Domestication by Genomic Selection

Cited by 26 publications

References 99 publications

A Genome‐Wide Association Study of Apple Quality and Scab Resistance

A Genome‐Wide Association Study of Apple Quality and Scab Resistance

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

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

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