Integrated high-density consensus genetic map of<i>Pyrus</i>and anchoring of the ‘Bartlett’ v1.0 (<i>Pyrus communis</i>) genome

Li, Leiting; Deng, Cecilia; Knäbel, Mareike; Chagné, David; Kumar, Satish; Sun, Jixiang; Zhang, Shaoling; Jun, Wu

doi:10.1093/dnares/dsw063

Cited by 26 publications

(46 citation statements)

References 45 publications

(80 reference statements)

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“…Genetic maps are essential tools for pear genetics and genomics research. Integrated simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)-based consensus genetic maps for pear based on common SSR markers between nine published maps were studied by Li et al (2017). A total of 5085 markers, including 1232 SSRs and 3853 SNPs, were localized on a consensus map spanning 3266.0 cM in total, with an average marker interval of 0.64 cM, which represents the highest density consensus map of pear to date.…”

Section: Introductionmentioning

confidence: 99%

“…A total of 5085 markers, including 1232 SSRs and 3853 SNPs, were localized on a consensus map spanning 3266.0 cM in total, with an average marker interval of 0.64 cM, which represents the highest density consensus map of pear to date. The integrated high-density SSR and SNP-based consensus genetic map provided new insights into the genetic structure patterns of pears (Li et al 2017). Kim et al (2015) aim was to determinate the taxonomic relationship among pear cultivars.…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity and similarity of pear (Pyrus communis L.) cultivars in Central Europe revealed by SSR markers

Kocsisne

Bolla

Anhalt-Brüderl

et al. 2020

Genet Resour Crop Evol

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The Hungarian pear gene bank, located and founded in Keszthely in 1981, contains 210 pear cultivars including regional cultivars, cultivars of foreign origin and standard commercial cultivars. There are some cultivars with synonym names in the pear gene bank and in other pear growing areas within the Hungary. The aim of our work was to systematically analyse the genotypes of Hungarian cultivars in the pear gene bank and to set up a robust protocol for molecular identification and the interpretation of data. Eighty-eight cultivars were analysed employing eight SSR primers resulting in a total of 216 alleles. Seventy-seven cultivars were thoroughly analysed. Among the samples 29 were considered to be diploids and 59 triploids. A genetic diversity analysis was computed based on a Neighbour-Joining algorithm and combined with a PCA indicating close genetic relationship and an overall high amount of genetic diversity among the samples tested. Similarities and very close relations were verified in our studies between different pear cultivar variants: 'Korai szagos' A and B, which were planted with the same name in the gene bank. Six different 'Császár körte' and three 'Köcsög körte' cultivars were compared. It was important to establish how close their relationship was. Some cultivars originating from the same regions were compared. The 'Mez} okövesdi 2 0 and '3 0 are in the same main branch, however their distance is larger, the number of common alleles is less than those of the two 'Erdélyi körte' cultivars.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic diversity and similarity of pear (Pyrus communis L.) cultivars in Central Europe revealed by SSR markers

Kocsisne

Bolla

Anhalt-Brüderl

et al. 2020

Genet Resour Crop Evol

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“…Another low‐density linkage map of Japanese pear ( Pyrus pyrifolia Nakai) was constructed using 335 SSRs and AFLP markers. Recently, high‐density genetic maps were constructed using SNP and SSR markers for mapping several fruit quality traits in Asian pear (Wu et al ., ) and to anchor the genome sequence of ‘Bartlett’ ( Pyrus communis , cultivated European pear) for synteny analysis between European and Asian pear (Li et al ., ). A dense genotyping array can be used to identify shared markers and integrate linkage maps of different pear species for comparative genetics analysis.…”

Section: Introductionmentioning

confidence: 97%

Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus)

Singh

Qin

et al. 2019

Plant Biotechnology Journal

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Summary Pear ( Pyrus ; 2 n = 34), the third most important temperate fruit crop, has great nutritional and economic value. Despite the availability of many genomic resources in pear, it is challenging to genotype novel germplasm resources and breeding progeny in a timely and cost‐effective manner. Genotyping arrays can provide fast, efficient and high‐throughput genetic characterization of diverse germplasm, genetic mapping and breeding populations. We present here 200K AXIOM ® Pyr SNP , a large‐scale single nucleotide polymorphism ( SNP ) genotyping array to facilitate genotyping of Pyrus species. A diverse panel of 113 re‐sequenced pear genotypes was used to discover SNP s to promote increased adoption of the array. A set of 188 diverse accessions and an F 1 population of 98 individuals from ‘Cuiguan’ × ‘Starkrimson’ was genotyped with the array to assess its effectiveness. A large majority of SNP s (166 335 or 83%) are of high quality. The high density and uniform distribution of the array SNP s facilitated prediction of centromeric regions on 17 pear chromosomes, and significantly improved the genome assembly from 75.5% to 81.4% based on genetic mapping. Identification of a gene associated with flowering time and candidate genes linked to size of fruit core via genome wide association studies showed the usefulness of the array in pear genetic research. The newly developed high‐density SNP array presents an important tool for rapid and high‐throughput genotyping in pear for genetic map construction, QTL identification and genomic selection.

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“…Pear (Pyrus spp.) is one of the economically and nutritionally valuable and popular rosaceous fruit crop being cultivated in temperate climates, it originated in the mountain regions of south-western China and have spread all over the world (1,2). It considered as the third most significant fruit crop after grapes and apples in temperate areas (3).…”

Section: Introducctionmentioning

confidence: 99%

Evaluation of genetic variations and phylogeny of the most popular pear (Pyrus communis L.) cultivars in Duhok city using AFLP markers

Ali

Othman²,

ZIBARI

et al. 2018

Innovaciencia

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Introduction: Genotyping and evaluation of genetic variation and polymorphic information content of the locally cultivated pear (Pyrus communis L.) might play an important role in building the genetic bank. These are also immensely important for present and future pear breeding program in the region. Methods: In the current study, AFLP markers have been employed to estimate the level of genetic diversity and to assess the phylogeny among the seven most popular pear cultivars in Duhok city. Results: Eight selective primer combinations generated a total of 653 AFLP fragments from which 445 (68.2%) fragments were polymorphic. The number of visible amplified products per primer combination were varied and ranged from 66 to 96 bands. The highest percentage of polymorphism (78.4%) was observed by the primer pair P174/M182, while the lowest percentage of polymorphism (58.6%) was observed by the primer pair P174/M100. The highest PIC (0.85) was obtained with the primer combination P174/ M182, while, the lowest PIC (0.49) was obtained by the primer combination P174/M307. The genetic distance was ranged from 0.1348 (between Danimarki and Amreki cultivars) to 0.3131 (between Italy and Zaafaran2 cultivars). Based on the AFLP data, all the seven pear genotypes were successfully clustered into two separate clusters (C1 and C2) with an out-group of Itali cultivar. Conclusions: Overall, it can be concluded that there was high polymorphism among the studied genotypes. Also, it can be stated that the AFLP was a reliable and a powerful technique in genotyping and discriminating of respective pear cultivars.Evaluación de variantes genéticas y filogenia de la pera común (Pyrus communis L.) cultivada en la ciudad Duhok empleando AFLP como marcadores moleculares Check for updatesHow to cite this paper: Ali S H., Othman H E., Zibari P A A., Jubrael J M S. Evaluation of genetic variations and phylogeny of the most popular pear (Pyrus communis L.) cultivars in Duhok city using AFLP markers, Duhok, Iraq. Innovaciencia. 2018; 6(1): 1-10.

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Integrated high-density consensus genetic map ofPyrusand anchoring of the ‘Bartlett’ v1.0 (Pyrus communis) genome

Cited by 26 publications

References 45 publications

Genetic diversity and similarity of pear (Pyrus communis L.) cultivars in Central Europe revealed by SSR markers

Genetic diversity and similarity of pear (Pyrus communis L.) cultivars in Central Europe revealed by SSR markers

Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus)

Evaluation of genetic variations and phylogeny of the most popular pear (Pyrus communis L.) cultivars in Duhok city using AFLP markers

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