Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools

AbstractMaize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.

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Genetic variation analysis of melon (Cucumis melo L. ‘Tacapa Gold’) using inter-simple sequence repeat

10.1063/5.0017611 ◽

2020 ◽

Author(s):

Budi Setiadi Daryono ◽

Fadilla Husnun ◽

Dian Sartika

Keyword(s):

Genetic Variation ◽

Simple Sequence Repeat ◽

Cucumis Melo ◽

Inter Simple Sequence Repeat ◽

Variation Analysis ◽

Sequence Repeat ◽

Cucumis Melo L ◽

Simple Sequence

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On genetic diversity in caraway: Genotyping of a large germplasm collection

PLoS ONE ◽

10.1371/journal.pone.0244666 ◽

2020 ◽

Vol 15 (12) ◽

pp. e0244666

Author(s):

Daniel von Maydell ◽

Heike Lehnert ◽

Thomas Berner ◽

Evelyn Klocke ◽

Wolfram Junghanns ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genome Size ◽

Phylogenetic Trees ◽

Germplasm Collection ◽

Genotyping By Sequencing ◽

Gene Pools ◽

History Of ◽

Winter Annual ◽

Neighbor Network

Caraway (Carum carvi) is a widespread and frequently used spice and medicinal plant with a long history of cultivation. However, due to ongoing climatic changes, the cultivation is becoming increasingly risky. To secure caraway cultivation in future, timely breeding efforts to develop adapted material are necessary. Analysis of genetic diversity can accompany this process, for instance, by revealing untapped gene pools. Here, we analyzed 137 accessions using genotyping by sequencing (GBS). Hence, we can report a broad overview of population structure and genetic diversity of caraway. Population structure was determined using a principal coordinate analysis, a Bayesian clustering analysis, phylogenetic trees and a neighbor network based on 13,155 SNPs. Genotypic data indicate a clear separation of accessions into two subpopulations, which correlates with the flowering type (annual vs. biennial). Four winter-annual accessions were closer related to biennial accessions. In an analysis of molecular variance, genetic variation between the two subpopulations was 7.84%. In addition, we estimated the genome size for 35 accessions by flow cytometry. An average genome size of 4.282 pg/2C (± 0.0096 S.E.) was estimated. Therefore, we suggest a significantly smaller genome size than stated in literature.

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Touch me carefully: a step towards understanding morphological diversity in the South American spiny sunflowers (Compositae, Barnadesioideae)

Phytotaxa ◽

10.11646/phytotaxa.518.2.3 ◽

2021 ◽

Vol 518 (2) ◽

pp. 109-142

Author(s):

PAOLA DE LIMA FERREIRA ◽

ALEXANDRE ANTONELLI ◽

MILTON GROPPO

Keyword(s):

South America ◽

Morphological Diversity ◽

South American ◽

Woody Vines ◽

Patagonian Steppe ◽

Secondary Center ◽

Center Of Diversity ◽

Taxonomic Changes ◽

Phylogenetic Hypotheses ◽

Secondary Center Of Diversity

The subfamily Barnadesioideae (Compositae) is endemic to South America, comprising 10 genera and 80 species of mostly spiny herbs, subshrubs, shrubs, trees, or woody vines distributed from Venezuela to Argentina. Three genera, Dasyphyllum (27 species), Chuquiraga (22 spp.) and Barnadesia (19 spp.) contain 85% of the species, while the other seven genera (Archidasyphyllum, Arnaldoa, Doniophyton, Duseniella, Fulcaldea, Huarpea, and Schlechtendalia) are represented by up to three species each. Most species are found in xeric areas in the Andean and Patagonian regions—as in the Páramos, Puna and Patagonian steppe vegetation—with a secondary center of diversity in eastern South America. Previous phylogenetic hypotheses have clarified the relationships within the subfamily, showing that there are many non-monophyletic groups in different taxonomic ranks. As a result, taxonomic changes have been proposed over recent decades in order to reflect classifications comprising only monophyletic groups. In the present study, we provide a generic synopsis of the subfamily Barnadesioideae based on the most recent generic circumscriptions, including a key, expanded morphological descriptions, information on geographical distribution and habitat, photographs and taxonomic notes for all genera.

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Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

International Journal of Molecular Sciences ◽

10.3390/ijms22136722 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6722

Author(s):

Do Yoon Hyun ◽

Raveendar Sebastin ◽

Gi-An Lee ◽

Kyung Jun Lee ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Variability ◽

Cucumis Melo ◽

Systematic Approach ◽

Genome Wide Association Study ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Phenotypic Traits ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Cucumis Melo L

Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.

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Hybridization for increased yield and nutritional content of snake melon (Cucumis melo L. var. flexuosus)

Plant Genetic Resources ◽

10.1017/s1479262110000067 ◽

2010 ◽

Vol 8 (2) ◽

pp. 127-131 ◽

Cited By ~ 10

Author(s):

Sudhakar Pandey ◽

N. P. S. Dhillon ◽

A. K. Sureja ◽

Dilbag Singh ◽

Ajaz A. Malik

Keyword(s):

Ascorbic Acid ◽

Genetic Variation ◽

Cucumis Melo ◽

Nutritional Content ◽

Botanical Variety ◽

First Report ◽

Intraspecific Genetic Variation ◽

Cucumis Melo L

This is the first report on increasing yield and nutritional content of snake melon (Cucumis melo L. var. flexuosus) by exploiting intraspecific genetic variation of genetically diverse melons. Inbred snake melon ‘Punjab Long melon 1’ (PLM1) was hybridized with five genetically diverse inbred melons: KP 7 (var. momordica), AM 72 (var. acidulus), ‘Arya 1’ (var. chate), 04-02 (var. tibish) and ‘Punjab Wanga’ (unknown botanical variety). The parents and hybrids were evaluated at three locations for nine traits. Hybrids PLM1 × 04-02 and PLM1 × ‘Punjab Wanga’ exhibited significant (P0.05) heterosis for the number of marketable fruits per plant, and ascorbic acid and carotenoid contents of marketable fruits.

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Morphological and Molecular Variation in a Collection of Eggplants from a Secondary Center of Diversity: Implications for Conservation and Breeding

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.130.1.54 ◽

2005 ◽

Vol 130 (1) ◽

pp. 54-63 ◽

Cited By ~ 45

Author(s):

Jaume Prohens ◽

José M. Blanca ◽

Fernando Nuez

Keyword(s):

Gene Diversity ◽

Solanum Melongena ◽

Germplasm Conservation ◽

Aflp Markers ◽

Cultivar Group ◽

Cultivar Groups ◽

Secondary Center ◽

Center Of Diversity ◽

Morphological Differences ◽

Secondary Center Of Diversity

Eggplant (Solanum melongena L.) was introduced by the Arabs into Spain. Since then, many local cultivars have arisen. These materials are grouped in four cultivar groups: “round,” “semi-long,” “long,” and “listada de Gandía.” We studied the morphological and molecular [amplified fragment length polymorphism (AFLP)] diversity of a collection of 28 Spanish traditional cultivars of eggplant. Four eggplant accessions from different origins were used as controls and three scarlet eggplant (Solanum aethiopicum L.) accessions as outgroups. Morphology and AFLP markers showed that S. melongena and S. aethiopicum are separate taxonomic entities, and that, compared to controls, Spanish eggplants are very variable, indicating that the Iberian Peninsula can be regarded as a secondary center of diversity. Morphological differences were found among cultivar groups in traits other than those used for the grouping although, in some cases, accessions from different cultivar groups shared a similar general morphology. Eggplant cultivar groups also showed some genetic differences, which are revealed in the gene diversity statistics (GST = 0.30). Nonetheless, no individual AFLP markers specific and universal to one cultivar group could be found. “Round” cultivars were genetically more diverse than the other cultivar groups. A positive correlation (r = 0.68) was found between morphological and molecular distances. However, correlations between geographical and either morphological or molecular distances were low. Results suggest that evolution of eggplants in Spain has involved frequent hybridizations and a frequent movement and exchange of seeds. Structure of diversity among regions indicates that most of the diversity can be collected in single selected regions. All these results have important implications in eggplant germplasm conservation and breeding.

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