Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing

Su, Wen‐Jin; Wang, Lianjun; Lei, Jian; Chai, Shasha; Liu, Yi; Yang, Yuanyuan; Yang, Xinsun; Chen, Jiao

doi:10.1371/journal.pone.0172066

Cited by 50 publications

(47 citation statements)

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“…The principal coordinate analysis has been widely used to represent genetic diversity in breeding programs in species such as maize (Van Inghelandt et al, 2010), sweet sorghum (Murray, Rooney, Hamblin, Mitchell, & Kresovich, 2009), rice (Choudhury et al, 2014;Roy et al, 2015), sweet potato (Su et al, 2017), and barley (Ferreira et al, 2016), among others. In all these works, associations among genotypes were revealed with the principal coordinate analysis.…”

Section: Comparison Of Techniquesmentioning

confidence: 99%

Comparison of projection of distance techniques for genetic diversity studies

et al. 2019

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The objective of this study was to compare different graphical dispersion analysis techniques in two- or three-dimensional planes. In this study, the data from different published works were used in order to determine the best methodology for analyzing the genetic diversity of different species. In this study, efficiency is measured by the amount of original distance absorbed by the projection of distances technique, which in the case of major components is equal to the amount of total variation originally available and retained by the principal components used for dispersion purposes. The projection of dissimilarity measurement technique, principal component analysis (PCA), and principal coordinate analysis (PCoA) were used. Considering the analysis by means of three orthogonal axes, the graphical dispersion efficiency was 82.22 for PCA, 87.22 for PCoA, and 85.25 for the projection of distances technique. For the 2D analysis, considering the two main axes, the mean dispersion efficiency was 69.90 for the PCA, 75.06 for the projection technique, and 78.16 for PCoA. Considering the studies carried out with experimental data of six different species, it is concluded that the principal coordinate analysis is superior.

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Section: Comparison Of Techniquesmentioning

confidence: 99%

Comparison of projection of distance techniques for genetic diversity studies

et al. 2019

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“…There have been many recent studies on the genetic diversity of sweetpotato collection around the world, including Africa (Elameen et al, 2008;Kagimbo et al, 2018;Ngailo et al, 2016;Selaocoe et al, 2019;Tumwegamire et al, 2011;Zawedde et al, 2015), Asia (Fajardo et al, 2002;He et al, 2006;Luo et al, 2016;Rahajeng and Rahayuningsih, 2017;Soegianto et al, 2011;Su et al, 2017;Zhang et al, 2014) , 2008;Zhang et al, 2000), and North America (Jarret and Austin, 1994;Rodriguez-Bonilla et al, 2014;Wadl et al, 2018). From these studies, it has been generally accepted that there is an abundance of genetic diversity in sweetpotato germplasm collections worldwide (Gichuki et al, 2003;Gr€ uneberg et al, 2015;Su et al, 2017;Wadl et al, 2018;Yang et al, 2015); however, smaller geographic collections may show a narrower range of genetic diversity due to inbreeding or other factors (Elameen et al, 2008;Hao et al, 2007;Meng et al, 2018). Within the USDA, ARS sweetpotato collections, there are multiple gene pools and clustering of accessions into geographical groups (Su et al, 2017;Wadl et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…From these studies, it has been generally accepted that there is an abundance of genetic diversity in sweetpotato germplasm collections worldwide (Gichuki et al, 2003;Gr€ uneberg et al, 2015;Su et al, 2017;Wadl et al, 2018;Yang et al, 2015); however, smaller geographic collections may show a narrower range of genetic diversity due to inbreeding or other factors (Elameen et al, 2008;Hao et al, 2007;Meng et al, 2018). Within the USDA, ARS sweetpotato collections, there are multiple gene pools and clustering of accessions into geographical groups (Su et al, 2017;Wadl et al, 2018). However, the wide variation of leaf characters shown in this study attests to the extensive genetic diversity of the USDA, ARS sweetpotato germplasm collection .…”

Section: Discussionmentioning

confidence: 99%

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Phenotypic Variation in Leaf Morphology of the USDA, ARS Sweetpotato (Ipomoea batatas) Germplasm Collection

Jackson¹,

Harrison²,

Jarret³

et al. 2020

horts

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During 2012–14, 737 sweetpotato, Ipomoea batatas (L.) Lam. (Convolvulaceae), plant introduction (PI) accessions from the U.S. Department of Agriculture, Agricultural Research Service (USDA, ARS) sweetpotato germplasm collection were evaluated for several phenotypic leaf and plant characteristics, and a photographic record of each accession was made. Data were prepared for placement in the USDA, ARS Germplasm Resources Information Network (GRIN) database and the sweetpotato ontology. The parameters recorded for each genotype were canopy coverage, vine length, general leaf outline, leaf lobing, shape of the central leaf lobe, number of leaf points, leaf petiole length, leaf width, leaf length, leaf width × length, and leaf width/length (aspect ratio). The data indicate that there is wide genetic diversity for vegetative phenotypic characteristics within the USDA, ARS sweetpotato germplasm collection. This study provides important phenotype information for the USDA, ARS sweetpotato collection that has been lacking and can be used for curation of the collection and by researchers and breeders working with this important global food crop.

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“…In recent years, SNP markers using a high-throughput sequencing technique have gained popularity in genetic mapping because of their stability, heritability, low cost, high-throughput efficiency and abundant genetics variations (Guo et al 2015). Specific-locus amplified fragment sequencing (SLAF-seq) markers is a high-throughput technique that has been widely adopted in different species for multiple purposes, including genetic diversity and population structure in sweet potato (Su et al 2017) and genome-wide association studies in rapeseed (Zhou et al 2017). In the last 5 years, SLAF-seq has been used successfully for construction of high-density genetic maps in many crops, including tea (Ma et al 2015), tree peony (Cai et al 2015), sorghum (Ji et al 2017), sweet osmanthus (He et al 2017) and poplars (Fang et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Construction of an SNP-based high-density genetic map for Japanese plum in a Chinese population using specific length fragment sequencing

Zhang

Xiao

Liu

et al. 2020

Tree Genetics & Genomes

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The Japanese plum (Prunus salicina Lindl.) is one of the most important stone fruit crops in China. High-density linkage map is valuable resources which enhance functional genomics and genetic breeding studies. So far several Japanese plum linkage maps have been reported using different kinds of molecular markers; however, the marker numbers and chromosome coverage are limited. Recently, a newly developed strategy which genome sequencing towards specific-locus amplified fragments (SLAF) markers, has been proven to be powerful for rapid genotyping of genome-wide markers and for high-density genetic map construction. In this study, SLAF was used to genotype markers with 114 F1 seedlings from the '09-16' × 'Fortune' cross. Suitable SLAF markers (160,344 out of 343,436,902 pair-end reads) were chosen to conduct genetic map construction, 16.31% of which were polymorphic. The overall integrated map contained 3,341 high quality SLAFs and 720 loci that were grouped in eight genetic linkage groups with a total length of 869.9 cM and an average distance of 1.21 cM, and only five gaps with a genetic distance > 5 cM between adjacent markers occurred in linkage group (LG) 3 and LG6. The number of markers with each LG ranged from 82.3 cM (LG3) to 138.3 cM (LG1). Aligning the map against the peach reference genome sequence (Prunus persica L.) indicated a strictly co-linear relationship between the LGs and peach genome, demonstrating the markers on ours LGs were well ordered. Overall, our studies identified large-scale of genetic markers and constructed high-density linkage maps for Japanese plum, which will obviously provide a solid foundation for marker-assisted selection and sequence assembly of the Japanese plum reference genome. Keywords Japanese plum. Genetic linkage map. Single nucleotide polymorphism. Specific length fragment sequencing Prunophora, genus Prunus, the Rosaceae family (Topp et al. 2012). The Japanese plum is a crop tree species native to China and it is widely cultivated from 23°N (the Guangxi and Yunnan provinces) to 45°N (Heihongjiang province). Due to its rich nutrients and unique flavour, the Japanese plum was popular in China, where the yield was the highest in the world (6,663,165 tonnes). Other major Japanese plumproducing countries include the USA (392,537 tonnes), followed by India (261,903 tonnes), Mexico (77,931 tonnes) and Japan (23,000 tonnes). In the Southern hemisphere plum production is dominated by Chile (294,873 tonnes) followed by Argentina (156,084 tonnes), South Africa (81,463 tonnes) and Australia (17,992 tonnes), also based on Japanese plum production (http://faostat.fao.org). The highest plum production in China over the last century came from native cultivars, since they had good flavour and were able to adapt to complex environments, though they had Qiu-ping Zhang and Xiao Wei contributed equally to this work. Communicated by D. Chagné

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Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing

Cited by 50 publications

References 50 publications

Comparison of projection of distance techniques for genetic diversity studies

Comparison of projection of distance techniques for genetic diversity studies

Phenotypic Variation in Leaf Morphology of the USDA, ARS Sweetpotato (Ipomoea batatas) Germplasm Collection

Construction of an SNP-based high-density genetic map for Japanese plum in a Chinese population using specific length fragment sequencing

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