Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing

Niu, Suzhen; Koiwa, Hisashi; Song, Qinfei; Qiao, Dahe; Chen, Juan; Zhao, Degang; Chen, Zhengwu; Wang, Ying; Zhang, Tianyuan

doi:10.7717/peerj.8572

Cited by 21 publications

(20 citation statements)

References 57 publications

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“…GBS has been used to analyze the population structure of maize [ 48 ], common bean ( Phaseolus vulgaris L. ) [ 44 ], wheat [ 49 ], and tea [ 15 , 50 ]. A previous study reported that 390.3 Gb clean data was obtained from 415 tea accessions and there was an average of 0.94 Gb clean data per accession.…”

Section: Discussionmentioning

confidence: 99%

“…Here, the core set was used to detect novel variations, select superior varieties, and furnish optimal germplasms because it consists of relatively smaller populations with comparatively higher genetic diversity [ 62 ]. Core collection development has been applied for cowpea [ 63 ], alpine plum [ 64 ], walnut [ 65 ], tea [ 50 , 57 ] and other plants. However, no core collection has yet been developed for the cultivated-type tea accessions in Guizhou Plateau.…”

Section: Discussionmentioning

confidence: 99%

“…The ‘maximum length subtree’ function was used to develop the core collection for tea as previously described. The threshold and development steps of the core collections were fully described in a previous report [ 50 ].…”

Section: Methodsmentioning

confidence: 99%

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Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

et al. 2022

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Background Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau. Results We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies. Conclusions The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

et al. 2022

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“…The core collection was used for detecting the novel variation, selecting excellent varieties, and providing the excellent germplasms for breeders by using smaller populations and greater genetic diversity [53]. So far, development of core collection was widely used in many plants, such as cowpea [54], alpine plum [55], walnut [56], tea plant [27,48] and so on. However, development of the core collection of cultivated-type tea accessions from Guizhou Plateau has not been reported.…”

Section: Development Core Collectionmentioning

confidence: 99%

Population Structure Analysis Revealed Water or Ancient Hub-induced Genetic Diversity of Cultivated-type Tea Plants in Guizhou Plateau

Zhong¹,

Song²,

Bai³

et al. 2021

Preprint

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Background Tea plants originated from the southwest of China. Guizhou is one of the origin center of tea plants, which is rich in tea plant germplasm resources. However, the distribution characteristics and transmission model of tea plant were still unclear. Results We collected 253 cultivated-type tea plant accessions from Guizhou plateau and analyzed the genetic diversity, PCA, phylogenetic, population structure, LD, and development of core collection using the genotyping-by-sequencing (GBS) approach. A total of 112,072 high-quality SNPs were identified, which was further used to analyze the genetic diversity and population structure. In this study, we found that the genetic diversity in cultivated-type tea accessions of PR Basin were significantly higher than that in cultivated-type tea accessions of YR Basin. Moreover, four groups, including three pure groups (CG-1, CG-2 and CG-3) and one admixture group (CG-4), were identified based on population structure analysis, which was verified by PAC and phylogenetic analysis. Our results showed that the highest GD and Fst values were found in CG-2 vs CG-3, followed by CG-1 vs CG-2 and CG-1 vs CG-3. The lowest GD and Fst values were detected in CG-4 vs CG-1, CG-4 vs CG-2, and CG-4 vs CG-3. Conclusions This study provided the evidence to confirm the contribution of PR and YR Basins and ancient hub road section to the transmission of cultivated-type tea accessions in Guizhou plateau. The genetic diversity, population structure and core collection revealed by our study will benefit further genetic studies, germplasm protection, and breeding.

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“…With the development of bioinformatic methods, many softwares for selecting core collections were developed and released based on the above strategies, such as MSTRAT, PowerCore, and Core Hunter3 (De Beukelaer et al, 2018;Liu et al, 2018;Gouesnard et al, 2001;Kim et al, 2007). The Core Hunter3 software is widely used to construct core collections in many species (De Beukelaer et al, 2018;Corak et al, 2019;Niu et al, 2020;Milner et al, 2019;Lv et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Construction and Genetic Analysis of a Worldwide Core Collection of Rapeseed

Guo

Yan

et al. 2021

Preprint

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Rapeseed (Brassica napus) is an important oilseed crop, which is widely planted in the world. In a previous study, we collected 991 accessions of rapeseed from the worldwide germplasm and revealed genetic polymorphisms within these germplasm by whole-genome resequencing. However, management of such a large amount of accessions is time-consuming, laborious and costly. Therefore, we constructed a core collection of rapeseed consisting of 300 worldwide accessions based on their genetic diversity. Compared with 991 accessions, the worldwide core collection showed similar geographic distribution, the proportion of three ecotypes, nucleotide diversity and the associated SNPs of flowering time. Besides, we identified FT ortholog (BnaA02g12130D) and FLC ortholog (BnaA10g22080D) responsible for flowering time and ecotype differentiation through selective sweep analysis and genome-wide association analysis (GWAS) of flowering time using the rapeseed core collection. FT and FLC are two well-known genes regulating flowering time in Arabidopsis. These results indicate that the worldwide core collection can represent the genetic diversity of 991 worldwide accessions, which could be more efficiently used for phenotypic and genetic studies in rapeseed.

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Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing

Cited by 21 publications

References 57 publications

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau

Population Structure Analysis Revealed Water or Ancient Hub-induced Genetic Diversity of Cultivated-type Tea Plants in Guizhou Plateau

Construction and Genetic Analysis of a Worldwide Core Collection of Rapeseed

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