Differentiation and genetic diversity of Phaseolus lunatus wild populations from Chiapas, Mexico, and their genetic relationships with MI and MII groups

Background. Understanding the genetic structure of wild relatives of domesticated species is crucial for its conservation and to elucidate the sites of crop domestication. Lima bean is one of the five domesticated Phaseolus species and Mexico is one of its centers of domestication. Recent studies showed the existence of two wild gene pools (MI and MII) of this species in Mexico and suggested that their genetic divergence occurred in southeast Mexico.Question. Did MI and MII groups diverged around the Isthmus of Tehuantepec, Mexico?Studied species. Lima bean: Neotropical plant species, herbaceous, with an annual/short life cycle and with autogamous tendency.Study site and years of study. Seven wild populations were collected in 2012 in the State of Chiapas, México, area underrepresented in previous studies.Methods. Genetic diversity and grouping patterns of collected populations and their relationship to MI and MII groups were analyzed at eight microsatellite loci.Results. High genetic structure (FST: 0.42 to 0.96) and a high level of genetic diversity (HE = 0.48) were found. The analyses, and presence of admixed populations in MI and MII, suggested that the genetic divergence of these groups is an ongoing process centered around the Isthmus of Tehuantepec.Conclusions. Our results support the hypothesis that MI and MII groups diverged around the Isthmus of Tehuantepec; however, sampling should be increased both at population and genomic levels, to determine the precise organization of the genetic diversity of wild P. lunatus from Mexico.

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Genetic Relationships among Cultivars and Landraces of Lima Bean (Phaseolus lunatus L.) as Measured by RAPD Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.120.2.300 ◽

1995 ◽

Vol 120 (2) ◽

pp. 300-306 ◽

Cited By ~ 45

Author(s):

James Nienhuis ◽

Jan Tivang ◽

Paul Skroch ◽

Joao B. dos Santos

Keyword(s):

Genetic Distance ◽

Genetic Relationships ◽

Major Gene ◽

Rapd Marker ◽

Lima Bean ◽

The United States ◽

Geographic Region ◽

Phaseolus Lunatus ◽

Gene Pools ◽

Size Number

Knowledge of relative genetic distance among genotypes is useful in a breeding program because it permits organization of germplasm resources. Genetic distance (GD) was estimated among 65 Phaselous lunatus L.. accessions, which included 4 large-seeded and 7 small-seeded cultivars and 54 germplasm accessions (landrace's) from the Caribbean and North, Central, and South America. Based on 125 polymorphic random amplification polymorphic DNA (RAPD) bands, two major clusters, which generally correspond in seed size and geographic region to [be Mesoamerican and Andean gene pools, were observed among the landraces (GD = 0.726 ± 0.041). Four Fordhook cultivars and a landrace from the United States formed a separate cluster that is more distantly related to the small- (GD) = 0.561 ± 0.039) than to the large-seeded cluster (GD = 0.303 ± 0.022). The mean GD between the Andean and Mesoamerican (0.726), Mesoamerican and Fordhook (0.561), and Andean and Fordhook (0.303) clusters were all significant. The significant GD between the Andean and Mesoamerican groups supports the hypothesized existence of two major gene pools in lima bean. The RAPD marker diversity of the Mesoamerican group was the largest (0.1 10), followed by the Andean (0.097) and Ford hook (0.062) groups. The plot of the relationship between the coefficient of variation (cv) and sample size (number of bands) indicates that cvs as low as 10% for estimating CD between Andean and Mesoamerican lima bean accessions can be achieved by sampling as few as 100 bands.

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Structure and Genetic Diversity of Wild Populations of Lima Bean (Phaseolus lunatus L.) from the Yucatan Peninsula, Mexico

Crop Science ◽

10.2135/cropsci2005.05-0081 ◽

2006 ◽

Vol 46 (3) ◽

pp. 1071-1080 ◽

Cited By ~ 19

Author(s):

Jaime Martínez-Castillo ◽

Daniel Zizumbo-Villarreal ◽

Paul Gepts ◽

Patricia Delgado-Valerio ◽

Patricia Colunga-GarcíaMarín

Keyword(s):

Genetic Diversity ◽

Yucatan Peninsula ◽

Lima Bean ◽

Phaseolus Lunatus ◽

Wild Populations ◽

Yucatán Peninsula

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The Brazilian lima bean landraces: conservation and breeding

10.21203/rs.3.rs-242568/v1 ◽

2021 ◽

Author(s):

Carolline de Jesús Pires ◽

Marcones Ferreira Costa ◽

Maria Imaculada Zucchi ◽

Regina Lucia Ferreira-Gomes ◽

José Baldin Pinheiro ◽

...

Keyword(s):

Genetic Diversity ◽

Molecular Characterization ◽

Genetic Divergence ◽

Polymorphic Information Content ◽

Lima Bean ◽

Optimization Method ◽

Morphological Characterization ◽

Phaseolus Lunatus ◽

Lima Beans ◽

On Farm

Abstract Brazil is one of the countries with the greatest genetic diversity in lima beans ( Phaseolus lunatus L.), which has been maintained both on farm and in germplasm banks. The knowledge of this diversity in the country is extremely important for developing a strategy for use and conservation. The objective of this study was characterizing landraces lima bean accessions from different regions in Brazil . Twenty two accessions conserved in the Phaseolus Germplasm Bank from UFPI (Piauí-Brazil) were characterized with 37 agro-morphological descriptors and 15 microsatellite markers. In the agro-morphological characterization, the maximum value of genetic divergence was obtained for the pair UFPI-262 and UFPI-252 (D = 88.74). The UPGMA grouping made it possible to form four groups. Tocher's optimization method enabled the formation of 10 groups. Regarding molecular characterization, 10 loci presented polymorphism, and the number of alleles per locus varied from two to seven. The Polymorphic Information Content (PIC) varied from 0.0767 to 0.7240. The loci GATS91 and PVat001 were highly informative and can be indicate for further studies involving the lima bean. The genetic diversity found (He = 0.316) was higher than that reported in the Yucatán Peninsula, a region indicated as a center of diversity for lima bean. Thus, the agro-morphological and molecular characterization were efficient in quantifying the genetic divergence between the studied accessions. The data found in this research provide a valuable resource for geneticists to subsidize breeding programs involving the lima bean.

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Comparative analysis of Genetic Diversity among Pod Vegetables Genetic Resources Potential in Indonesia Revealed by ISSR Markers

Jurnal Hortikultura Indonesia ◽

10.29244/jhi.10.3.161-172 ◽

2019 ◽

Vol 10 (3) ◽

pp. 161-172

Author(s):

Ria Rif’atunidaudina ◽

Sobir ◽

Awang Maharijaya

Keyword(s):

Genetic Diversity ◽

Vigna Unguiculata ◽

Genetic Relationships ◽

Phenotypic Variability ◽

Lima Bean ◽

Issr Markers ◽

Similarity Coefficient ◽

Phaseolus Lunatus ◽

Mucuna Pruriens ◽

Velvet Bean

Cowpea (Vigna unguiculata ssp unguiculata), yardlong bean (Vigna unguiculata ssp sesquipedalis), Bambara groundnut (V.subterranea), lima bean (Phaseolus lunatus), bush bean (P. vulgaris), jack bean (Canavalia ensiformis), velvet bean (Mucuna pruriens) and winged bean (Psophocarpus tetragonolobus) are the important pod vegetable of the legume crop in Indonesia. These crops have a high economic and nutritional value. Its dry seeds are rich in proteins just like soybeans that can support human health and future food supply. The genetic diversity among different pod vegetables is not very well known. The objectives of this research were to determine the genetic relationships among different pod vegetable species based on ISSR markers. 32 accessions were analyzed by 11 ISSR primers. The result showed that the ISSR marker generated 80 DNA band with the polymorphism rate of 100% and the informative primers were PKBT 3 and PKBT 6. The result of cluster analysis and PCA analysis grouped all 32 accessions of the vegetable pod into eight clusters, indicating that the majority of the accession of a given species tend to group. Gower's similarity coefficient among all accessions varied from 0.425 to 0.988, and from 0.444 to 0.700 at the species level. The ISSR markers revealed the close relatedness between V. subterranea - C. ensiformis species, while the greatest distance was found between the P. vulgaris - M. pruriens species. Such a determination of relatedness is useful for a better understanding of the relationships among different pod vegetable species, which are generally considered to be a complex group with high phenotypic variability. Keywords: clustering, genetic distance, polymorphism, pulses, similarity coefficient

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Biodiversity studies in Phaseolus species by DNA barcoding

Genome ◽

10.1139/g11-018 ◽

2011 ◽

Vol 54 (7) ◽

pp. 529-545 ◽

Cited By ~ 19

Author(s):

Silvia Nicolè ◽

David L. Erickson ◽

Daria Ambrosi ◽

Elisa Bellucci ◽

Margherita Lucchin ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Barcoding ◽

Genetic Relationships ◽

Phaseolus Lunatus ◽

Gene Pools ◽

Common Beans ◽

Intergenic Spacers ◽

Rdna Sequences ◽

Multilocus Approach ◽

Pure Lines

The potential of DNA barcoding was tested as a system for studying genetic diversity and genetic traceability in bean germplasm. This technique was applied to several pure lines of Phaseolus vulgaris L. belonging to wild, domesticated, and cultivated common beans, along with some accessions of Phaseolus coccineus L., Phaseolus lunatus L., and Vigna unguiculata (L.) Walp. A multilocus approach was exploited using three chloroplast genic regions (rbcL, trnL, and matK), four intergenic spacers (rpoB-trnC, atpBrbcL, trnT-trnL, and psbA-trnH), and nuclear ITS1 and ITS2 rDNA sequences. Our main goals were to identify the markers and SNPs that show the best discriminant power at the variety level in common bean germplasm, to examine two methods (tree based versus character based) for biodiversity analysis and traceability assays, and to evaluate the overall utility of chloroplast DNA barcodes for reconstructing the origins of modern Italian varieties. Our results indicate that the neighbor-joining method is a powerful approach for comparing genetic diversity within plant species, but it is relatively uninformative for the genetic traceability of plant varieties. In contrast, the character-based method was able to identify several distinct haplotypes over all target regions corresponding to Mesoamerican or Andean accessions; Italian accessions originated from both gene pools. On the whole, our findings raise some concerns about the use of DNA barcoding for intraspecific genetic diversity studies in common beans and highlights its limitations for resolving genetic relationships between landraces and varieties.

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Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha44210391 ◽

2016 ◽

Vol 44 (2) ◽

pp. 431-436 ◽

Cited By ~ 6

Author(s):

Masoumeh YOUSEFIAZARKHANIAN ◽

Ali ASGHARI ◽

Jafar AHMADI ◽

Behvar ASGHARI ◽

Ali Ashraf JAFARI

Keyword(s):

Genetic Diversity ◽

Genetic Polymorphisms ◽

Genomic Dna ◽

Rapd Markers ◽

Genetic Relationships ◽

Genetic Variations ◽

Molecular Techniques ◽

Wild Populations ◽

Similarity Coefficients ◽

The World

The genus Salvia includes an enormous assemblage of nearly 1,000 species dispersed around the world. Due to possible threats to this genus, there is an immediate requirement to evaluate the diversity of its wild populations. ISSR and RAPD molecular techniques were used to evaluate the genetic relationships among twenty-one ecotypes of eight Salvia species. Amplification of genomic DNA using 23 primers (15 RAPD and eight ISSR) produced 280 bands, of which 91% were polymorphic. The results of marker parameters showed no clear difference between two marker systems. It was generally observed that both ISSR and RAPD markers had similar efficiency in detecting genetic polymorphisms with remarkable ability to differentiate the closely related ecotypes of Salvia. Neiâ€™s similarity coefficients for these techniques ranged from 0.48 to 0.98. Based on the results of clustering, PCoA and AMOVA, the genetic diversity between and within species was confirmed. So, conservation and domestication of the genus Salvia must be due to levels of genetic variations.

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Genetic diversity in accessions of lima bean (Phaseolus lunatus L.) determined from agro-morphological descriptors and SSR markers for use in breeding programs in Brazil

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01272-8 ◽

2021 ◽

Author(s):

Carolline de Jesús Pires ◽

Marcones Ferreira Costa ◽

Maria Imaculada Zucchi ◽

Regina Lucia Ferreira-Gomes ◽

José Baldin Pinheiro ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Lima Bean ◽

Phaseolus Lunatus ◽

Morphological Descriptors ◽

Breeding Programs

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Population genetic structure and variability in Lindera glauca (Lauraceae) indicates low levels of genetic diversity and skewed sex ratios in natural populations in mainland China

PeerJ ◽

10.7717/peerj.8304 ◽

2020 ◽

Vol 8 ◽

pp. e8304 ◽

Cited By ~ 2

Author(s):

Biao Xiong ◽

Limei Zhang ◽

Shubin Dong ◽

Zhixiang Zhang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Isolation By Distance ◽

Sex Ratios ◽

Mainland China ◽

Small Sample ◽

Chloroplast Microsatellites ◽

Wild Populations ◽

Haplotype Networks ◽

Low Levels

Lindera glauca (Lauraceae) is a tree of economic and ecological significance that reproduces sexually and asexually via apomictic seeds. It is widely distributed in the low-altitude montane forests of East Asia. Despite the potential implications of a mixed reproductive system in terms of genetic diversity, few studies have focused on this aspect. In this study, the genetic structure of wild populations of L. glauca was investigated via genetic analyses. Overall, 13 nuclear microsatellites (nSSRs) and five chloroplast microsatellites (cpSSRs) were used to genotype 300 individual plants, taken from 20 wild populations (a small sample size in some wild populations is due to the limitation of its specific reproduction, leading to certain limitations in the results of this study) and two cultivated populations ranging across nearly the entire natural distribution of mainland China. The populations exhibited low levels of genetic diversity (nSSR: AR = 1.75, Ho = 0.32, He = 0.36; cpSSR: Nb = 2.01, Hrs = 0.40), and no significant effect of isolation by distance between populations existed, regardless of marker type (nSSR: R2 = 0.0401, P = 0.068; cpSSR: R2 = 0.033, P = 0.091). Haplotype networks showed complex relationships among populations, and the H12 haplotype was predominant in most populations. Analyses of molecular variance obtained with nuclear markers (Fsc = 0.293, FST = 0.362) and chloroplast markers (Fsc = 0.299, FST = 0.312) were similar. The migration ratio of pollen flow versus seed flow in this study was negative (r = −1.149). Results suggest that weak barriers of dispersal between populations and/or the similarity of founders shared between neighbors and distant populations are indicative of the gene flow between populations more likely involving seeds. Wild L. glauca in mainland China was inferred to have highly skewed sex ratios with predominant females. In addition, some populations experienced a recent bottleneck effect, especially in Gujianshan, Chongqing, and southwest China (population GJS). It is suggested that few wild male individuals should be conserved in order to maintain overall genetic diversity in the wild populations of this species. These findings provide important information for the sustainable utilization and preservation of the overall genetic diversity of L. glauca.

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GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽

10.7251/agreng1603110k ◽

2016 ◽

Vol 1 (3) ◽

Author(s):

Veronika KUKUČKOVÁ ◽

Nina MORAVČÍKOVÁ ◽

Radovan KASARDA

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

The State ◽

Most Probable Number ◽

Pedigree Data ◽

Probable Number ◽

Expected Heterozygosity ◽

High Level ◽

The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

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Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

10.1101/2020.10.08.331140 ◽

2020 ◽

Author(s):

Brenda G. Díaz ◽

Maria I. Zucchi ◽

Alessandro. Alves-Pereira ◽

Caléo P. de Almeida ◽

Aline C. L. Moraes ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Structure ◽

Genetic Relationships ◽

Geographical Area ◽

Taxonomic Classification ◽

Genomic Diversity ◽

Productive Capacity ◽

Snp Analysis ◽

Genetic Population

AbstractAcrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

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