Impact of fruit shape selection on genetic structure and diversity uncovered from genome-wide perfect SNPs genotyping in eggplant

Liu, Weilun; Qian, Zongwei; Zhang, Jian; Yang, Jingjing; Ming-sheng, WU; Barchi, Lorenzo; Zhao, Hongchang; Sun, Honghe; Yanling, Cui; Wen, Changlong

doi:10.1007/s11032-019-1051-y

Cited by 17 publications

(10 citation statements)

References 52 publications

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“…(2017) used a genotyping by sequencing (GBS) approach to detect SNPs polymorphisms in eggplant, working with a set of 76 accessions of species belonging to the brinjal ( S. melongena ), scarlet ( S. aethiopicum ) and gboma ( S. macrocarpon ) eggplant complexes, to detect the genetic relationships within and between the genepools. Moving to 2019, Liu et al. (2019b) employed the SNP genotyping technique (SNP-seq) to validate genome-wide perfect SNPs in eggplant.…”

Section: Genotyping Tools and Their Evolutionmentioning

confidence: 99%

“…, Acquadro et al (2017 used a genotyping by sequencing (GBS) approach to detect SNPs polymorphisms in eggplant, working with a set of 76 accessions of species belonging to the brinjal (S. melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplant complexes, to detect the genetic relationships within and between the genepools. Moving to , Liu et al (2019b employed the SNP genotyping technique (SNP-seq) to validate genome-wide perfect SNPs in eggplant. This high-throughput SNP genotyping technology allowed a genome-wide association study based on the 219 SNPs identified five associated SNPs located near the SUN and OVATE homologs, which had conserved function in controlling the fruit shape.…”

Section: Eggplantmentioning

confidence: 99%

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Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

Martina,

De Rosa,

Magon

et al. 2024

Front. Plant Sci.

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This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.

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Section: Genotyping Tools and Their Evolutionmentioning

confidence: 99%

Section: Eggplantmentioning

confidence: 99%

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

Martina,

De Rosa,

Magon

et al. 2024

Front. Plant Sci.

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“…In this study, genome-wide perfect SSRs and perfect SNPs were selected for genetic analysis in melon. These have been successfully applied in other vegetables, such as cucumber [10,14], eggplant [15], pepper [16], and watermelon [17].…”

Section: Efficient Genotyping Tools Of Perfect Ssr/snps In Melonmentioning

confidence: 99%

“…With the development of high-throughput sequencing, the genome of melon and numerous melon accessions have been sequenced and characterized using the nextgeneration sequence platform providing a foundation for the selection of perfect SSRs/SNPs in melon [5,[11][12][13]. In earlier studies, genome-wide perfect SSRs and SNPs were efficiently established and evaluated for variety identification in cucumber [10,14], eggplant [15], pepper [16], and watermelon [17]. Therefore, the application of DNA fingerprinting in melon varieties using genome-wide perfect SSRs and SNPs is reasonable.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity analysis and variety identification using SSR and SNP markers in melon

Zhang

Yang

et al. 2023

BMC Plant Biol

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Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R2 = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of ‘Jingyu’ and ‘Jingmi’ series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon.

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“…These studies validated a number of previously identified QTLs affecting anthocyanin pigmentation, as well as fruit and plant morphology; further, due to the wide genetic diversity that existed in the panel of genotypes, several new marker-trait associations were identified. Another association mapping study based on 219 SNPs applied to a set of 377 eggplant accessions identified five SNPs near the SUN and OVATE homologs of tomato, respectively encoding for a protein promoting fruit elongation and a protein playing a negative role in the growth and elongation of fruit (Liu et al, 2019b).…”

Section: B Mapped Genes and Qtlsmentioning

confidence: 99%

Genomics and Marker-Assisted Improvement of Vegetable Crops

Šimko

Jia

Venkatesh

et al. 2021

Critical Reviews in Plant Sciences

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Vegetables are an integral part of the human diet worldwide. Traditional breeding approaches have been used extensively to develop new cultivars of vegetables with desirable characteristics, including resistance/tolerance to biotic and abiotic stresses, high yield, and an elevated content of compounds beneficial to human health. The technological progress since the early 1980s has revolutionized our ability to study and manipulate genetic variation in crop plants. The development of high-throughput sequencing platforms and accompanying analytical methods have led to sequencing and assembly of a large number of plant genomes, construction of dense and ultra-dense molecular linkage maps, identification of structural variants, and application of molecular markers in breeding programs. Linkage mapping and genome-wide association mapping studies have been used to identify chromosomal locations of genes and QTLs associated with plant phenotypic variations important for crop improvement. This review provides up-to-date information on the status of genomics and marker-assisted improvement of vegetable crops with the focus on tomato, pepper, eggplant, lettuce, spinach, cucumber, and chicory. For each vegetable crop, we present the most recent information on genetic resources, mapping populations, genetic maps, genome sequences, mapped genes and QTLs, the status of marker-assisted selection and genomic selection, and discuss future research prospects and application of novel techniques and approaches.

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Impact of fruit shape selection on genetic structure and diversity uncovered from genome-wide perfect SNPs genotyping in eggplant

Cited by 17 publications

References 52 publications

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

Genetic diversity analysis and variety identification using SSR and SNP markers in melon

Genomics and Marker-Assisted Improvement of Vegetable Crops

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