Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai)

Yamamoto, Takatsugu; Terakami, Shingo; Takada, Norio; Nishio, Sogo; Onoue, Noriyuki; Nishitani, Chikako; Kunihisa, Miyuki; Inoue, Eiichi; Iwata, Hiroyoshi; Hayashi, Takeshi; Itai, Akihiro; Saito, Toshihiro

doi:10.1270/jsbbs.64.351

Cited by 71 publications

(65 citation statements)

References 39 publications

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“…The potential of GWAS was examined in pear with a population of 76 Japanese pear cultivars: significant associations detected in the GWAS agreed well with the results of biparental linkage/QTL mapping (Iwata, Hayashi, Terakami, Takada, Sawamura et al, 2013). Two significant associations of marker genotypes with harvest time detected in GWAS were also detected in biparental QTL mapping (Yamamoto et al, 2014). A significant association of marker genotypes with resistance to black spot disease was located close to the disease susceptibility genes Ani and Ana, which had been detected in biparental linkage mapping (Terakami et al, 2007).…”

Section: Genome-wide Association Studiessupporting

confidence: 56%

“…A significant association of marker genotypes with resistance to black spot disease was located close to the disease susceptibility genes Ani and Ana, which had been detected in biparental linkage mapping (Terakami et al, 2007). The results of GWAS and biparental mapping also agreed in fruit skin colour (Yamamoto et al, 2014). These results suggest that GWAS will be useful for the detection of QTLs for important agronomic traits, and will provide an effective alternative to the traditional time-consuming QTL mapping.…”

Section: Genome-wide Association Studiesmentioning

confidence: 56%

“…Saeed et al (2014) performed QTL analysis for fruit friction discolouration and related traits (fruit firmness, polyphenol oxidase activity, concentrations of phenolic compounds and ascorbic acid) using two populations derived from Asian Â European pears, and identified a total of 221 QTLs for 22 phenotyped variables. Yamamoto et al (2014) performed QTL mapping of seven fruit traits (harvest time, fruit skin colour, flesh firmness, fruit weight, acid content, total soluble solids content, and preharvest fruit drop) using a population derived from a Japanese pear cross, and detected 12 QTLs. Some of these 12 QTLs were detected in genome-wide association studies (GWAS) described below.…”

Section: Linkage/qtl Mapping For Marker-assisted Selectionmentioning

confidence: 99%

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Acceleration of Forest and Fruit Tree Domestication by Genomic Selection

Isik¹,

Kumar²,

Martínez-García³

et al. 2015

Advances in Botanical Research

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Section: Genome-wide Association Studiessupporting

confidence: 56%

Section: Genome-wide Association Studiesmentioning

confidence: 56%

Section: Linkage/qtl Mapping For Marker-assisted Selectionmentioning

confidence: 99%

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Acceleration of Forest and Fruit Tree Domestication by Genomic Selection

Isik¹,

Kumar²,

Martínez-García³

et al. 2015

Advances in Botanical Research

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“…In the middle of LG-D, significant QTLs (qtl-HARVESTKu-D and qtl-HARVEST-T43-D) were detected in both the Kx709 and Px43 populations, and their LOD scores and percentages of phenotypic variance explained were similar, suggesting that these QTLs were controlled by the same gene and probably had high reliability and general versatility. Many QTLs for fruit harvesting day have been identified in several fruit tree species (Eduardo et al, 2011;Kenis et al, 2008;Kunihisa et al, 2014;Liebhard et al, 2003;Yamamoto et al, 2014), and broad-sense heritability of fruit harvesting day was higher than that of other fruit traits Nishio et al, 2014;Yamada et al, 1993). Thus, both the QTLs for fruit harvesting day identified in earlier studies and the HARVEST QTLs identified here may have been identified owing to their high heritability.…”

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confidence: 99%

Identification of QTLs for Agronomic Traits in the Japanese Chestnut (<i>Castanea crenata</i> Sieb. et Zucc.) Breeding

et al. 2018

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The chestnut (genus Castanea) has a long juvenile phase, and breeders have to wait three years or more to evaluate nut traits. Therefore, molecular markers associated with genes of interest are required to speed the selection process in chestnut breeding programs. Genetic linkage maps of the Japanese chestnut were constructed using two breeding populations derived from crosses between 'Kunimi' and breeding line '709-034' (Kx709), and between 'Porotan' and 'Tsukuba-43' (Px43). Maps of the four parents and two integrated maps (one representing each cross) were constructed using 443 simple sequence repeat markers (SSRs) and 554 single-nucleotide polymorphism markers. In the Kx709 integrated map, which was the most saturated of the six maps, 12 linkage groups were identified that covered 668.1 cM with an average distance of 0.8 cM between loci. Using anchor SSRs, these six maps were successfully aligned to the Chinese chestnut consensus map. We evaluated eight important traits, including several nut traits, to identify molecular markers associated with these traits. At least one significant quantitative trait locus (QTL) was detected for each of the eight traits (21 in total). Logarithm of odds (LOD) values and phenotypic variance explained by these QTLs ranged from 2.60 to 7.90 and from 11.6% to 29.1%, respectively. In the Kx709 population analysis, several QTLs for nut harvesting date (HARVEST) and pericarp splitting (SPLIT) were detected. Under the assumption that the effects of these QTLs are additive, the percentage of total phenotypic variance explained by the combination of QTLs was high for both HARVEST (47.5%-60.8%) and SPLIT (33.4%-41.7%). Because these mapping populations and their parents are essential materials for Japanese chestnut breeding programs, these QTLs will soon be used for marker-assisted selection to improve breeding efficiency.

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“…However, GWASs are just beginning to be applied to fruit tree species, with only a few species having being analyzed to date (Myles et al 2011). Yamamoto et al (2014) conducted GWASs to detect significant associations between 162 markers and nine agronomic traits, including harvest time, resistance to black spot disease, firmness of flesh, fruit size, fruit shape in the longitudinal section, acid content, total soluble solid content, number of spurs, and tree vigor, which are important in pear production. GWASs using the 76 Japanese pear cultivars have detected four markers showing significant associations with three traits: resistance to black spot disease, harvest time, and the number of spurs.…”

Section: Genome-wide Association Studies (Gwass) In Pyrusmentioning

confidence: 99%

Current Status of Knowledge and Research Perspectives in Korean Pear Genomics

Kim

2015

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT The pear (Pyrus spp.) is most important fruit crop in the world. The genus Pyrus belongs to the subfamily Maloideae in the Rosaceae family and contains at least 22 primary species; however, only a few species, including P. pyrifolia, P. ussuriensis, P. bretschneideri, and P. communis have been utilized for fruit production. In Korea, awareness of the importance of the fruit industry and fruit tree breeding is low, and there is little support for genetic and genomic studies of fruit trees. In foreign countries, studies have focused on obtaining genomic information of fruit crops and the development of important agronomic trait-related molecular markers, providing a genomic framework for fruit tree breeding. Although Korea does not actively participate in research on the genomics of fruit trees, it is not far behind other countries in terms of technology and is therefore still competitive in research and development. The resequencing of 'Whangkeumbae' and 'Minibae' pears has been performed using the Illumina Hiseq 2000 platform as a part of the Biogreen 21 project, offering novel, rapid methods for identification of molecular marker, such as single nucleotide polymorphisms, insertion-deletions, and simple sequence repeats, through next-generation sequencing (NGS) technology. These NGS-based molecular markers are useful for genetic studies of Asian pears, e.g., for construction of genetic linkage maps, mapping of quantitative trait loci, and marker-assisted selection.

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Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai)

Cited by 71 publications

References 39 publications

Acceleration of Forest and Fruit Tree Domestication by Genomic Selection

Acceleration of Forest and Fruit Tree Domestication by Genomic Selection

Identification of QTLs for Agronomic Traits in the Japanese Chestnut (<i>Castanea crenata</i> Sieb. et Zucc.) Breeding

Current Status of Knowledge and Research Perspectives in Korean Pear Genomics

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