Genetic diversity and population structure in Beninese pigeon pea [Cajanus cajan (L.) Huth] landraces collection revealed by SSR and genome wide SNP markers

Zavinon, Fiacre; Adoukonou‐Sagbadja, Hubert; Keilwagen, Jens; Lehnert, Heike; Ordon, Frank; Perović, Dragan

doi:10.1007/s10722-019-00864-9

Cited by 34 publications

(29 citation statements)

References 51 publications

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“…Rani et al [34] using 10 RAPD and 10 ISSR markers for 42 genotypes reported high PIC values of 0.73 and 0.77, respectively. Using genotyping-by-sequencing (GBS) and single nucleotide polymorphisms (SNPs) a lower PIC value of 0.25 was reported [19]. The low levels of polymorphism reported in this study are in agreement with previous findings of several researchers [35][36][37], who reported low polymorphism in cultivated pigeonpea genotypes.…”

Section: Discussionsupporting

confidence: 92%

“…The estimated average PIC value (0.46) recorded in the current study was similar to PIC value (0.49) reported by Sousa et al [18], lower than a mean PIC (0.57) reported by Zavinon et al [19] but relatively higher than the average PIC value of 0.37 as reported by Bohra et al [30]. Similarly, Singh et al [31] observed a PIC value of 0.515.…”

Section: Discussionsupporting

confidence: 85%

“…Among the DNA molecular markers, the simple sequence repeat (SSR) markers have been found to be the most suitable for use in pigeonpea [16]. A number of studies have been reported using SSR markers for detecting population structure and reconstructing the evolutionary history of the species [17][18][19]. The SSR markers are chosen because of high polymorphism, detection of multi-allelic variation, co-dominance, they are reproducible, they are easy to detect by polymerase chain reaction (PCR), are relatively abundant with a uniform coverage, require small amount of DNA and act as a universal genetic marker for the genetic reagent mapping [14,15,20].…”

Section: Introductionmentioning

confidence: 99%

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Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Kimaro

Melis

Sibiya

et al. 2020

Plants

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Understanding the genetic diversity present amongst crop genotypes is an efficient utilization of germplasm for genetic improvement. The present study was aimed at evaluating genetic diversity and population structure of 48 pigeonpea genotypes from four populations collected from diverse sources. The 48 pigeonpea entries were genotyped using 33 simple sequence repeat (SSR) markers that are polymorphic to assess molecular genetic diversity and genetic relatedness. The informative marker combinations revealed a total of 155 alleles at 33 loci, with an average of 4.78 alleles detected per marker with the mean polymorphic information content (PIC) value of 0.46. Population structure analysis using model based revealed that the germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 53.3% of genetic variation existed within individuals. Relatively low population differentiation was recorded amongst the test populations indicated by the mean fixation index (Fst) value of 0.032. The Tanzanian pigeonpea germplasm collection was grouped into three major clusters. The clustering pattern revealed a lack of relationship between geographic origin and genetic diversity. This study provides a foundation for the selection of parental material for genetic improvement.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 85%

Section: Introductionmentioning

confidence: 99%

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Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Kimaro

Melis

Sibiya

et al. 2020

Plants

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“…SSRs are well known and widely used in studies of the genetic diversity and population structure of species 44 – 46 . Compared with gSSRs, EST-SSRs are functional molecular markers with the advantages of easier and more efficient development, lower cost and more interspecific transferability 15 – 17 .…”

Section: Discussionmentioning

confidence: 99%

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Zang

Xie³

et al. 2020

Sci Rep

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Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.

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“…Polymorphic pigeonpea microsatellites have been widely reported (Odeny et al, 2009;Saxena et al, 2010;Bohra et al, 2011;Sarika et al, 2013). Zavinon et al (2020) studied genetic diversity and population structure in 77 Benin landraces, using 30 loci. Sharma et al (2018) used 33 loci to assess genetic diversity among a set of Indian accessions of male sterile, maintainer and germplasm lines.…”

Section: Introductionmentioning

confidence: 99%

Research Article Genetic diversity and structure of pigeonpea germplasm assessed by microsatellite markers

Costa¹,

Santos²

2021

Genet. Mol. Res.

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The pigeonpea is an important grain legume in various regions of the world. It is a pulse that is cultivated mainly by small farmers in semi-arid tropical regions for various purposes, including food security, livestock feed, and agroforestry systems. We examined the genetic diversity and structure of 73 pigeonpea accessions from 10 origins, including regions of Brazil, Central America, and India. Allelic diversity and polymorphism, molecular analysis of variance (AMOVA), Bayesian analysis (Structure) and a dendrogram were estimated based on data concerning 11 microsatellite loci. AMOVA revealed wide genetic differentiation among the pigeonpea populations, with F ST ranging from 0.22 to 0.25. Expected heterozygosity in the accessions was greater than the observed heterozygosity in eight of the 11 loci, with the observed heterozygosity ranging from 0.06 to 0.55. Polymorphic information content ranged from 0.13 to 0.67 among the 11 loci. Genetic similarity among pigeonpea accessions ranged from 0.26 to 0.93, indicating considerable variability among them, with the formation of three groups, one of which included all Brazilian accessions. Two groups were formed in the Structure analysis, indicating reduced allele sharing between the populations of Northeast Brazil and other populations. This information highlights the importance of incorporating germplasm from the Brazilian ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 20 (1): gmr18807 A.E da S. Costa et al. 2Northeast into pigeonpea breeding programs in Brazil, to increase the variability in germplasm collections.

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Genetic diversity and population structure in Beninese pigeon pea [Cajanus cajan (L.) Huth] landraces collection revealed by SSR and genome wide SNP markers

Cited by 34 publications

References 51 publications

Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Full-length transcriptome sequencing analysis and development of EST-SSR markers for the endangered species Populus wulianensis

Research Article Genetic diversity and structure of pigeonpea germplasm assessed by microsatellite markers

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