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

Abstract

An accurate depiction of the genetic relationship, the development of core collection, and genome-wide association analysis (GWAS) are key for the effective exploitation and utilization of genetic resources. Here, genotyping-by-sequencing (GBS) was used to characterize 415 tea accessions mostly collected from the Guizhou region in China. A total of 30,282 high-quality SNPs was used to estimate the genetic relationships, develop core collections, and perform GWAS. We suggest 198 and 148 accessions to represent the core set and mini-core set, which consist of 47% and 37% of the whole collection, respectively, and contain 93-95% of the total SNPs. Furthermore, the frequencies of all alleles and genotypes in the whole set were very well retained in the core set and mini-core set. The 415 accessions were clustered into 14 groups and the core and the mini-core collections contain accessions from each group, species, cultivation status and growth habit. By analyzing the significant SNP markers associated with multiple traits, nine SNPs were found to be significantly associated with four leaf size traits, namely MLL, MLW, MLA and MLSI (P < 1.655E−06). This study characterized the genetic distance and relationship of tea collections, suggested the core collections, and established an efficient GWAS analysis of GBS result. Development of corecollections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing. PeerJ 8:e8572 E, Barreneche T. 2016. Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars. BMC Plant Biology 16(1):49 . 2017. Genetic diversity, population structure, and linkage disequilibrium of a core collection of Ziziphus jujuba assessed with genome-wide SNPs developed by genotyping-by-sequencing and SSR markers. L. 2013. Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources. PLOS ONE 8(4):e59714 DOI 10.1371/journal.pone.0059714. Coan MMD, Senhorinho HJC, Pinto RJB, Scapim CA, Warburton ML. 2018. Genomewide association study of resistance to ear rot by in a tropical field maize and popcorn core collection. Crop Science 58(2):564-578 DOI 10.2135/cropsci2017.05.0322. Cunff LL, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, Adam-Blondon AF, Boursiquot JM, This P. 2008. Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa. BMC Plant Biology 8(1):31 Egbadzor KF, Ofori K, Yeboah M, Aboagye LM, Opoku-Agyeman MO, Danquah EY, Offei SK. 2014. Diversity in 113 cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers. Springer Plus 3(1):541

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

“…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.…”

“…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.…”

“…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 ].…”

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

“…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.…”

Construction and Genetic Analysis of a Worldwide Core Collection of Rapeseed

“…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).…”