{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T15:01:55Z","timestamp":1787065315436,"version":"build-2736575974"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,3]],"date-time":"2022-11-03T00:00:00Z","timestamp":1667433600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013718","name":"Alliance for a Green Revolution in Africa","doi-asserted-by":"publisher","award":["PASS030"],"award-info":[{"award-number":["PASS030"]}],"id":[{"id":"10.13039\/100013718","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Knowledge of genetic interrelationships and grouping among pigeonpea germplasm collections is fundamental to selecting breeding parents with unique genetic constitutions. The objectives of this study were to assess the genetic diversity and genetic grouping present among 81 pigeonpea genotypes collected from Malawi, Tanzania and Kenya using 4122 single nucleotide polymorphism (SNP) markers and complementary morphological traits. The SNP markers and phenotypic traits revealed significant genetic variation among the assessed genotypes. The test genotypes were resolved into three distinct clusters based on both marker systems. The mean gene diversity and the polymorphic information content (PIC) were 0.14 and 0.11, suggesting moderate genetic differentiation among the genotypes. The analysis of molecular variance revealed that differences among populations accounted for only 2.7% of the variation, while within the population (among individuals) accounted for 97.3% of the variation. The results based on the DArT SNP genotyping complemented the phenotypic data and led to the selection of unique pigeonpea genotypes for effective breeding programs in Malawi and related agroecologies. This suggested that unique breeding populations could be created by identifying and selecting divergent individuals as parental lines. There is a need to create a new genetic variation or introgress genes from genetically unrelated parents to increase the genetic base of the current pigeonpea breeding populations.<\/jats:p>","DOI":"10.1371\/journal.pone.0275060","type":"journal-article","created":{"date-parts":[[2022,11,3]],"date-time":"2022-11-03T13:42:18Z","timestamp":1667482938000},"page":"e0275060","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":13,"title":["Genetic diversity and grouping of pigeonpea [Cajanus cajan Millspaugh] Germplasm using SNP markers and agronomic traits"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0605-271X","authenticated-orcid":true,"given":"Esnart Nyirenda","family":"Yohane","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2793-8392","authenticated-orcid":true,"given":"Hussein","family":"Shimelis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Laing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Admire","family":"Shayanowako","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,11,3]]},"reference":[{"issue":"3","key":"pone.0275060.ref001","first-page":"145","article-title":"Survey of pigeonpea production systems, utilization and marketing in semi-arid lands of Kenya","volume":"5","author":"G Mergeai","year":"2001","journal-title":"Biotechnology, Agronomy, Society and Environment"},{"key":"pone.0275060.ref002","doi-asserted-by":"crossref","unstructured":"Odeny DA, (editor). The potential of pigeonpea (Cajanus cajan (L.) Millsp.) in Africa. Natural resources forum; 2007: Wiley Online Library.","DOI":"10.1111\/j.1477-8947.2007.00157.x"},{"issue":"37","key":"pone.0275060.ref003","first-page":"107","article-title":"Measurement of N 2-fixation in field-grown pigeonpea [Cajanus cajan [56] Millsp.] using 15 N-labelled fertilizer","volume":"101","author":"JK Rao","year":"1987","journal-title":"Plant and Soil"},{"issue":"1\u20132","key":"pone.0275060.ref004","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/s11104-006-9006-6","article-title":"Yields and accumulations of N and P in farmer-managed intercrops of maize\u2013pigeonpea in semi-arid Africa","volume":"285","author":"FM Myaka","year":"2006","journal-title":"Plant and soil"},{"issue":"37","key":"pone.0275060.ref005","first-page":"33","article-title":"Assessment of biological nitrogen fixing potentials of pigeonpea genotypes intercropped with sorghum for soil fertility improvement in Southern Guinea Savanna of Nigeria","volume":"6","author":"O. Egbe","year":"2007","journal-title":"Agro-Science"},{"issue":"4954","key":"pone.0275060.ref006","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1126\/science.248.4954.477","article-title":"Phosphorus uptake by pigeon pea and its role in cropping systems of the Indian subcontinent","volume":"248","author":"A Noriharu","year":"1990","journal-title":"Science"},{"issue":"03","key":"pone.0275060.ref007","doi-asserted-by":"crossref","first-page":"279","DOI":"10.5958\/0975-6906.2015.00045.0","article-title":"From concept to field: Evolution of hybrid pigeonpea technology in India","volume":"75","author":"K. Saxena","year":"2015","journal-title":"Indian Journal of Genetics and Plant Breeding"},{"issue":"37","key":"pone.0275060.ref008","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/nbt.2022","article-title":"Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers","volume":"30","author":"RK Varshney","year":"2012","journal-title":"Nature biotechnology"},{"issue":"37","key":"pone.0275060.ref009","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1007\/s13562-011-0088-8","article-title":"The first draft of the pigeonpea genome sequence","volume":"21","author":"NK Singh","year":"2012","journal-title":"Journal of plant biochemistry and biotechnology"},{"issue":"37","key":"pone.0275060.ref010","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1007\/s10681-014-1142-0","article-title":"First information on heterotic groups in pigeonpea [Cajanus cajan [56] Millsp.]","volume":"200","author":"K Saxena","year":"2014","journal-title":"Euphytica"},{"issue":"37","key":"pone.0275060.ref011","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1017\/S1479262110000419","article-title":"Pigeonpea composite collection and identification of germplasm for use in crop improvement programmes","volume":"9","author":"HD Upadhyaya","year":"2011","journal-title":"Plant Genetic Resources"},{"issue":"9","key":"pone.0275060.ref012","doi-asserted-by":"crossref","first-page":"184","DOI":"10.19044\/esj.2018.v14n9p184","article-title":"Quantitative Analysis, Distribution and traditional management of pigeon pea [Cajanus cajan [56] Millsp.] landraces\u2019 diversity in Southern Benin","volume":"14","author":"F Zavinon","year":"2018","journal-title":"European Scientific Journal"},{"issue":"03","key":"pone.0275060.ref013","first-page":"341","article-title":"Narrowing yield gaps through genetic improvement for Fusarium wilt resistance in three pulse crops of the semi-arid tropics","volume":"45","author":"A Choudhary","year":"2013","journal-title":"SABRAO Journal of Breeding and Genetics"},{"issue":"37","key":"pone.0275060.ref014","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1023\/A:1015759318497","article-title":"Diversity in selected wild and cultivated species of pigeonpea using RFLP of mtDNA","volume":"125","author":"S Sivaramakrishnan","year":"2002","journal-title":"Euphytica"},{"issue":"37","key":"pone.0275060.ref015","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1590\/S0102-33062014000200007","article-title":"Using AFLP-RGA markers to assess genetic diversity among pigeon pea (Cajanus cajan) genotypes in relation to major diseases","volume":"28","author":"PG Pati","year":"2014","journal-title":"Acta Botanica Brasilica"},{"key":"pone.0275060.ref016","first-page":"1","article-title":"RAPD analysis among pigeon pea [Cajanus cajan [56] Millsp.] cultivars for their genetic diversity","volume":"1","author":"N Malviya","year":"2010","journal-title":"Genetic Engineering and Biotechnology Journal"},{"key":"pone.0275060.ref017","doi-asserted-by":"crossref","first-page":"1804","DOI":"10.20546\/ijcmas.2017.604.216","article-title":"Genetic diversity among Pigeonpea (Cajanus cajan L. Millsp.) genotypes using genic SSRs with putative function for drought tolerance","volume":"6","author":"B Sarkar","year":"2017","journal-title":"International Journal of Current Microbiology Applied Scince"},{"issue":"37","key":"pone.0275060.ref018","doi-asserted-by":"crossref","first-page":"e88568","DOI":"10.1371\/journal.pone.0088568","article-title":"Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs","volume":"9","author":"RK Saxena","year":"2014","journal-title":"PLoS One"},{"issue":"3","key":"pone.0275060.ref019","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1007\/s11032-009-9327-2","article-title":"Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)","volume":"26","author":"R Varshney","year":"2010","journal-title":"Molecular Breeding"},{"issue":"4","key":"pone.0275060.ref020","doi-asserted-by":"crossref","first-page":"e25","DOI":"10.1093\/nar\/29.4.e25","article-title":"Diversity arrays: a solid state technology for sequence information independent genotyping","volume":"29","author":"D Jaccoud","year":"2001","journal-title":"Nucleic Acids Research"},{"issue":"37","key":"pone.0275060.ref021","first-page":"1","article-title":"A 62K genic-SNP chip array for genetic studies and breeding applications in pigeonpea (Cajanus cajan L. Millsp.)","volume":"10","author":"S Singh","year":"2020","journal-title":"Scientific reports"},{"issue":"4","key":"pone.0275060.ref022","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1007\/s00122-006-0317-z","article-title":"Low level of genetic diversity in cultivated pigeonpea compared to its wild relatives is revealed by diversity arrays technology","volume":"113","author":"S Yang","year":"2006","journal-title":"Theoretical and Applied Genetics"},{"key":"pone.0275060.ref023","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.plantsci.2015.09.009","article-title":"Exciting journey of 10 years from genomes to fields and markets: some success stories of genomics-assisted breeding in chickpea, pigeonpea and groundnut","volume":"242","author":"RK Varshney","year":"2016","journal-title":"Plant Science"},{"issue":"11","key":"pone.0275060.ref024","doi-asserted-by":"crossref","first-page":"1682","DOI":"10.3390\/agronomy10111682","article-title":"Phenotypic Divergence Analysis in Pigeonpea [Cajanus cajan [56] Millspaugh] Germplasm Accessions","volume":"10","author":"EN Yohane","year":"2020","journal-title":"Agronomy"},{"key":"pone.0275060.ref025","doi-asserted-by":"crossref","first-page":"1878","DOI":"10.3389\/fpls.2020.587426","article-title":"Genome-wide DArTSeq genotyping and phenotypic based assessment of within and among accessions diversity and effective sample size in the diverse sorghum, pearl millet, and pigeonpea landraces","volume":"11","author":"V Allan","year":"2020","journal-title":"Frontiers in Plant Science"},{"key":"pone.0275060.ref026","unstructured":"IBPGR. Descriptors for pigeonpea [Cajanus cajan [56] Millsp.]. Italy, Rome: International Board of Plant Genetic Resouces; 1993."},{"key":"pone.0275060.ref027","unstructured":"IBM SPSS Statistics for Windows, Version 26.0. [Internet]. IBM Corp. 2019."},{"key":"pone.0275060.ref028","unstructured":"Maechler M, Rousseeuw P, Struyf A, Hubert M, Hornik K. cluster: Cluster analysis basics and extensions. R package version 2.1. 0. 2019."},{"key":"pone.0275060.ref029","unstructured":"Hastie T, Tibshirani R, Balasubramanian N, Chu G. impute: Imputation for microarray data. R package version 1.42. 0. 2017."},{"issue":"8","key":"pone.0275060.ref030","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1111\/2041-210X.12067","article-title":"diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors","volume":"4","author":"K Keenan","year":"2013","journal-title":"Methods in ecology and evolution"},{"issue":"37","key":"pone.0275060.ref031","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1111\/j.1471-8286.2005.01155.x","article-title":"GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research","volume":"6","author":"R Peakall","year":"2006","journal-title":"Molecular ecology notes"},{"issue":"37","key":"pone.0275060.ref032","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method","volume":"4","author":"DA Earl","year":"2012","journal-title":"Conservation genetics resources"},{"issue":"8","key":"pone.0275060.ref033","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study","volume":"14","author":"G Evanno","year":"2005","journal-title":"Molecular Ecology"},{"issue":"37","key":"pone.0275060.ref034","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: analyses of phylogenetics and evolution in R language","volume":"20","author":"E Paradis","year":"2004","journal-title":"Bioinformatics"},{"key":"pone.0275060.ref035","unstructured":"Garnier S, Ross N, Rudis B, Sciaini M, Scherer C. viridis: Default Color Maps from \u2018matplotlib\u2019. R package version 05. 2018;1."},{"issue":"37","key":"pone.0275060.ref036","doi-asserted-by":"crossref","first-page":"3718","DOI":"10.1093\/bioinformatics\/btv428","article-title":"dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering","volume":"31","author":"T. Galili","year":"2015","journal-title":"Bioinformatics"},{"issue":"37","key":"pone.0275060.ref037","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1093\/genetics\/162.2.861","article-title":"Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations","volume":"162","author":"M Knox","year":"2002","journal-title":"Genetics"},{"issue":"2","key":"pone.0275060.ref038","first-page":"191","article-title":"Phenotypic variability in Cowpea (Vigna unguiculate L. Walp) genotypes assessed with quantitative and qualitative characters","volume":"52","author":"N. Onwubiko","year":"2020","journal-title":"SABRAO J Breed Genet"},{"issue":"37","key":"pone.0275060.ref039","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1007\/s10722-006-9008-5","article-title":"Phenotypic diversity in the pigeonpea (Cajanus cajan) core collection","volume":"54","author":"H Upadhyaya","year":"2007","journal-title":"Genetic Resources and Crop Evolution"},{"key":"pone.0275060.ref040","first-page":"1","article-title":"Variability patterns in Ugandan pigeonpea landraces","volume":"7","author":"E Manyasa","year":"2009","journal-title":"Journal of SAT Agricultural Research"},{"issue":"377","key":"pone.0275060.ref041","first-page":"1","article-title":"New hypervariable SSR markers for diversity analysis, hybrid purity testing and trait mapping in pigeonpea [Cajanus cajan [56] Millspaugh]","volume":"8","author":"A Bohra","year":"2017","journal-title":"Frontiers in Plant Science"},{"key":"pone.0275060.ref042","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/S0065-2113(01)72012-3","article-title":"Genetics of flowering time in chickpea and its bearing on productivity in semiarid environments","volume":"72","author":"J Kumar","year":"2001","journal-title":"Advances in Agronomy"},{"issue":"3","key":"pone.0275060.ref043","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1093\/genetics\/89.3.583","article-title":"Estimation of average heterozygosity and genetic distance from a small number of individuals","volume":"89","author":"M. Nei","year":"1978","journal-title":"Genetics"},{"issue":"12","key":"pone.0275060.ref044","doi-asserted-by":"crossref","first-page":"e0243238","DOI":"10.1371\/journal.pone.0243238","article-title":"Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers","volume":"15","author":"W Nkhata","year":"2020","journal-title":"PLoS One"},{"key":"pone.0275060.ref045","first-page":"110","article-title":"Assessing the genetic diversity of cowpea [Vigna unguiculata [56] Walp.] germplasm collections using phenotypic traits and SNP markers","volume":"21","author":"N Nkhoma","year":"2020"},{"issue":"10","key":"pone.0275060.ref046","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.1534\/g3.114.012468","article-title":"Resolution of genetic map expansion caused by excess heterozygosity in plant recombinant inbred populations","volume":"4","author":"SK Truong","year":"2014","journal-title":"G3: Genes, Genomes, Genetics"},{"key":"pone.0275060.ref047","first-page":"137","article-title":"Pigeonpea: genetics","author":"K Saxena","year":"1990","journal-title":"The pigeonpea"},{"issue":"6D","key":"pone.0275060.ref048","first-page":"2249","article-title":"Genetic Diversity and Population Structure Analysis of Tropical Soybean (Glycine Max (L.) Merrill) using single","volume":"20","author":"T Obua","year":"2020","journal-title":"Nucleotide Polymorphic Marker. Global journal of science frontier research"},{"issue":"37","key":"pone.0275060.ref049","first-page":"1","article-title":"Population genetic diversity and fitness in multiple environments","volume":"10","author":"JA Markert","year":"2010","journal-title":"BMC evolutionary biology"},{"issue":"37","key":"pone.0275060.ref050","first-page":"996","article-title":"Heterozygosity mapping for human dominant trait variants","volume":"40","author":"A Imai\u2010Okazaki","year":"2019","journal-title":"Human Mutation"},{"key":"pone.0275060.ref051","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511808999","volume-title":"Introduction to conservation genetics","author":"R Frankham","year":"2002"},{"issue":"37","key":"pone.0275060.ref052","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1007\/s10535-008-0126-0","article-title":"Assessment of genetic diversity of pigeonpea cultivars using RAPD analysis","volume":"52","author":"PR Choudhury","year":"2008","journal-title":"Biologia Plantarum"},{"issue":"4","key":"pone.0275060.ref053","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.30848\/PJB2019-4(41)","article-title":"Genetic structure of pakistani oilseed brassica cultivars revealed by morphometric and microsatellite markers","volume":"51","author":"H Khurshid","year":"2019","journal-title":"Pakistan Journal of Botany"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0275060","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,10]],"date-time":"2023-03-10T21:41:01Z","timestamp":1678484461000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0275060"}},"subtitle":[],"editor":[{"given":"Tzen-Yuh","family":"Chiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,11,3]]},"references-count":53,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0275060","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,3]]}}}