Exploring Genetic Diversity and Population Structure in an International Panel of Pigeonpea (<i>Cajanus cajan</i> L. Millsp.)-Crop Breeding, Genetics and Genomics-CSCIED科技核心评价数据库-手机版

Exploring Genetic Diversity and Population Structure in an International Panel of Pigeonpea (Cajanus cajan L. Millsp.)

Exploring Genetic Diversity and Population Structure in an International Panel of Pigeonpea (Cajanus cajan L. Millsp.)

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DOI	10.20900/cbgg20250016
刊名	Crop Breeding, Genetics and Genomics CBGG
年，卷(期)	2025, 7(4)
作者	Mohammed Salah,Shruthi H. Belliappa,Naresh Bomma,Mahesh Pujar,Anilkumar Vemula,Sunil S. Gangurde,Manish K. Pandey,Victor O. Adetimirin,Prakash I. Gangashetty*,
作者单位	International Crops Research Institute for the Semi-Arid Tropics, Hyderabad 502324, Telangana, India ; Pan African University Life and Earth Sciences Institute (PAULESI), University of Ibadan, Ibadan 200001, Nigeria ;
摘要	Pigeonpea is an important legume cultivated in more than 25 tropical and sub-tropical countries, either as sole or as inter crop with finger millet, sorghum, pearl millet, maize or even with short duration legumes. It offers a rich source of variability in the form of wild species and germplasm, which could be used for brining favorable alleles for disease resistance and good agronomic traits. Pigeonpea [Cajanus cajan (L.) Millsp.] 248 reference set accessions were evaluated in an augmented design for assessing genetic variability and diversity for important agronomic attributes at ICRISAT, Patancheru. The morphological characterization revealed significant genetic variability among the accessions for traits studied, as shown by the significant (p < 0.0001) mean squares for the six traits through the analysis of variance (ANOVA). High heritability estimates (>70%) for all the six traits indicated that the selection can be highly responsive. Principal component analysis (PCA) identified key traits contributing to variability, with the first three components explaining 84.30% of the total variance. Cluster analysis based on morphological traits delineated six distinct groups, highlighting the diversity within the germplasm. Molecular characterization using 52,863 high-quality SNPs provided further insights into genetic diversity. The SNP analysis revealed moderate levels of polymorphism (average PIC = 0.36) and genetic diversity (mean He = 0.37). Population structure analysis suggested the presence of four main sub-populations (K = 4) with varying degrees of admixture. Analysis of Molecular Variance (AMOVA) indicated that the majority of genetic variation (87.01%) was found within populations, with moderate genetic differentiation (FST = 0.13) between the populations. The study identified several genetically distinct accessions that could serve as valuable resources for broadening the genetic base in pigeonpea breeding programs. These findings provide crucial insights for germplasm conservation, targeted breeding efforts, and the exploration of genetic diversity in pigeonpea, potentially leading to the development of more resilient and productive varieties.
Abstract	Pigeonpea is an important legume cultivated in more than 25 tropical and sub-tropical countries, either as sole or as inter crop with finger millet, sorghum, pearl millet, maize or even with short duration legumes. It offers a rich source of variability in the form of wild species and germplasm, which could be used for brining favorable alleles for disease resistance and good agronomic traits. Pigeonpea [Cajanus cajan (L.) Millsp.] 248 reference set accessions were evaluated in an augmented design for assessing genetic variability and diversity for important agronomic attributes at ICRISAT, Patancheru. The morphological characterization revealed significant genetic variability among the accessions for traits studied, as shown by the significant (p < 0.0001) mean squares for the six traits through the analysis of variance (ANOVA). High heritability estimates (>70%) for all the six traits indicated that the selection can be highly responsive. Principal component analysis (PCA) identified key traits contributing to variability, with the first three components explaining 84.30% of the total variance. Cluster analysis based on morphological traits delineated six distinct groups, highlighting the diversity within the germplasm. Molecular characterization using 52,863 high-quality SNPs provided further insights into genetic diversity. The SNP analysis revealed moderate levels of polymorphism (average PIC = 0.36) and genetic diversity (mean He = 0.37). Population structure analysis suggested the presence of four main sub-populations (K = 4) with varying degrees of admixture. Analysis of Molecular Variance (AMOVA) indicated that the majority of genetic variation (87.01%) was found within populations, with moderate genetic differentiation (FST = 0.13) between the populations. The study identified several genetically distinct accessions that could serve as valuable resources for broadening the genetic base in pigeonpea breeding programs. These findings provide crucial insights for germplasm conservation, targeted breeding efforts, and the exploration of genetic diversity in pigeonpea, potentially leading to the development of more resilient and productive varieties.
关键词	diversity; variability; population structure; pigeonpea; single nucleotide polymorphism (SNP)
KeyWord	diversity; variability; population structure; pigeonpea; single nucleotide polymorphism (SNP)
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相关文献

1.Khuntia D, Panda N, Mandal M, Swain P, Sahu SG, Pattanayak SK. Symbiotic effectiveness of acid tolerant nodulating rhizobia on growth, yield and nutrient uptake of pigeon pea (Cajanus cajan L.) in acidic alfisols. Int J Bio-Resour Stress Manag. 2022;13(4):403-10. doi: 10.23910/1.2022.2550.

2.Mekonen T, Tolera A, Nurfeta A, Bradford B, Mekasha A. Location and plant spacing affect biomass yield and nutritional value of pigeon pea forage. Agron J. 2022;114(1):228-47. doi: 10.1002/agj2.20803.

3.Susmitha D, Kalaimagal T, Senthil R, Vetriventhan M, Manonmani S, Jeyakumar P, et al. Grain nutrients variability in pigeonpea genebank collection and its potential for promoting nutritional security in dryland ecologies. Front Plant Sci. 2022;13:934296. doi: 10.3389/fpls.2022.934296.

4.Muniswamy SG, Singh N, Pandey S, Singh IP. Morphological characterization and genetic diversity among indigenous collections of pigeonpea
[Cajanus cajan (L.) Millsp]. Legume Res. 2022;46(9):1148-54. doi: 10.18805/LR-4806.

5.Sinha P, Singh VK, Saxena RK, Khan AW, Abbai R, Chitikineni A, et al. Superior haplotypes for haplotype‐based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). Plant Biotechnol J. 2020;18(12):2482-90. doi: 10.1111/pbi.13422.

6.Singh G, Singh I, Taggar GK, Rani U, Sharma P, Gupta M, et al. Introgression of productivity enhancing traits, resistance to pod borer and Phytopthora stem blight from Cajanus scarabaeoides to cultivated pigeonpea. Physiol Mol Biol Plants. 2020;26(7):1399-410. doi: 10.1007/s12298-020-00827-w.

7.Yohane EN, Shimelis H, Laing M, Shayanowako A. Genetic diversity and grouping of pigeonpea
[Cajanus cajan Millspaugh] germplasm using SNP markers and agronomic traits. PLoS ONE. 2022;17(11):e0275060. doi: 10.1371/journal.pone.0275060.

8.Zavinon F, Adoukonou-Sagbadja H, Keilwagen J, Lehnert H, Ordon F, Perovic D. Genetic diversity and population structure in Beninese pigeon pea
[Cajanus cajan (L.) Huth] landraces collection revealed by SSR and genome wide SNP markers. Genet Resour Crop Evol. 2020;67(1):191-208. doi: 10.1007/s10722-019-00864-9.

9.Muniswamy S, Lokesha R, Saxena R, Fakrudin B, Patel KY. Molecular dissection of genetic diversity in pigeonpea
[Cajanus cajan (L) Millsp.] minicore collection. Legume Res. 2019;42(1):32-8. doi: 10.18805/LR-3817.

10.Kumari K, Thamilarasi K, Ghosh J, Lohot VD, Ghosal S. Molecular diversity analysis of pigeonpea genotypes for scar marker development. Int J chem Stud, 2019;14:15.

11.Kinhoégbè G, Djèdatin G, Saxena RK, Chitikineni A, Bajaj P, Molla J, et al. Genetic diversity and population structure of pigeonpea (Cajanus cajan
[L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing. PLoS ONE. 2022;17(7):e0271565. doi: 10.1371/journal.pone.0271565.

12.Gadekar M, Jadhav R, Meshram M, Amarshettiwar S, Patil A, Nandanwar R. Molecular diversity study in CMS-A, maintainer-B and restorer-R lines in pigeon pea
[Cajanus cajan (L.) Millsp.]. Int J Curr Microbiol Appl Sci. 2017;6(12):500-7. doi: 10.20546/ijcmas.2017.612.061.

13.IBPGR, ICRISAT. Descriptors for pigeonpea
[Cajanus cajan (L.) Millsp.]. Rome (Italy): International Board for Plant Genetic Resources (IBPGR); Patancheru (Andhra Pradesh, India): International Crops Research Institute for the Semi-Arid Tropics (ICRISAT); 1993. p. 31.

14.SAS Inst. The SAS system for Windows. Release 9.2. Cary (NC, US): SAS Inst; 2010.

15.Allard RW. Principles of plant breeding. New York (NY, US): John Wiley and Sons Inc; 1960.

16.Jeffers JNR. Two case studies in the application of principal component analysis. J Appl Stat. 1967;16:225-36.

17.Mahalanobis PC. On the generalized distance in statistics. Proc Natl Inst Sci India. 1936;2(1):49-55.

18.Rao CR. Advanced statistical methods in biometric research. New York (NY, US): John Wiley and Sons Inc; 1952. p. 130-4.

19.Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945-59. doi: 10.1093/genetics/155.2.945.

20.Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23(19):2633-5. doi: 10.1093/bioinformatics/btm308.

21.Jombart T. Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics. 2008;24(11):1403-5. doi: 10.1093/bioinformatics/btn328.

22.Kamvar ZN, Tabima JF, Grünwald NJ. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ. 2014;2:e281. doi: 10.7717/peerj.281.

23.Saxena RK, von Wettberg E, Upadhyaya HD, Sanchez V, Songok S, Saxena K, et al. Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs. PLoS ONE. 2014;9(2):e88568. doi: 10.1371/journal.pone.0088568.

24.Zavinon F, Adoukonou-Sagbadja H, Bossikponnon A, Dossa H, Ahanhanzo C. Phenotypic diversity for agro-morphological traits in pigeon pea landraces
[(Cajanus cajan L.) Millsp.] cultivated in southern Benin. Open Agric. 2019;4(1):487-99. doi: 10.1515/opag-2019-0046.

25.Sousa ACB de, Godoy R, Sforça DA, Campos T de, Zucchi MI, Jank L, et al. Genetic diversity analysis among pigeonpea genotypes adapted to South American regions based on microsatellite markers. Scientia Agric. 2011;68(4):431-9. doi: 10.1590/S0103-90162011000400007.

26.Njung’e V, Deshpande S, Siambi M, Jones R, Silim S, De Villiers S. SSR genetic diversity assessment of popular pigeonpea varieties in Malawi reveals unique fingerprints. Electron J Biotechnol. 2016;21:65-71. doi: 10.1016/j.ejbt.2016.02.004.

27.Ceccarelli S. Efficiency of plant breeding. Crop Sci. 2015;55(1):87-97. doi: 10.2135/cropsci2014.02.0158.

28.Hill WG, Mackay TFC. D. S. Falconer and introduction to quantitative genetics. Genetics. 2004;167(4):1529-36. doi: 10.1093/genetics/167.4.1529.

29.Falconer DS. Introduction to quantitative genetics. London (UK): Oliver and Boyd; 1981. p. 340.

30.Hemavathy AT, Bapu JR, Priyadharshini C. Principal component analysis in pigeonpea
[Cajanus cajan (L.) millsp.]. Electron J Plant Breed. 2017;8:1133-9.

31.Hussain ME, Sharma S, Joel AJ, Ravikesavan R, Senthil N, Senthil A. Genetic variability of agronomic traits in extra-early maturing introgression lines (ILs) of pigeonpea
[Cajanus cajan (L.)]. Electron J Plant Breed. 2021;12:507-14.

32.Akshaya M, Geetha K, Nirmalakumari A, Sivakumar C, Sharavanan PT. Morphological characterization of pigeonpea genotypes using DUS descriptors. Electron J Plant Breed. 2023;14(2):448-57.

33.Ranjani MS, Jayamani P, Manonmani S, Latha KR, Sethuraman K. Genetic analysis and diversity in early duration pigeonpea (Cajanus cajan (L.) MillSp.) genotypes. Electron J Plant Breed. 2021;12(2):540-8.

34.Ojo BT, Togun AO, Abberton M, Oyatomi O, Dada OA. Morphological and molecular characterization of pigeon pea (Cajanus cajan (L.) Millsp.) for improved utilization. J Genet Eng Biotechnol Res. 2023;5(3):186-97.

35.Lynch M. Evolution of the mutation rate. Trends Genet. 2010;26(8):345-52. doi: 10.1016/j.tig.2010.05.003.

36.Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature. 2022;602(7895):101-5. doi: 10.1038/s41586-021-04269-6.

37.Luo G-H, Li X-H, Han Z-J, Zhang Z-C, Yang Q, Guo H-F, et al. Transition and transversion mutations are biased towards GC in transposons of Chilo suppressalis (Lepidoptera: Pyralidae). Genes. 2016;7(10):72. doi: 10.3390/genes7100072.

38.Thakur O, Randhawa GS. Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots. BMC Genomics. 2018;19(1):951. doi: 10.1186/s12864-018-5205-9.

39.Wondimu Z, Dong H, Paterson AH, Worku W, Bantte K. Genetic diversity, population structure, and selection signature in Ethiopian sorghum
[Sorghum bicolor L. (Moench)] germplasm. G3 (Bethesda). 2021;11(6):jkab087. doi: 10.1093/g3journal/jkab087.

40.Zhu YO, Siegal ML, Hall DW, Petrov DA. Precise estimates of mutation rate and spectrum in yeast. Proc Natl Acad Sci USA. 2014;111(22):E2310-8. doi: 10.1073/pnas.1323011111.

41.Mohammadi SA, Prasanna BM. Analysis of genetic diversity in crop plants—salient statistical tools and considerations. Crop Sci. 2003;43(4):1235-48. doi: 10.2135/cropsci2003.1235.

42.Araus JL, Slafer GA, Royo C, Serret MD. Breeding for yield potential and stress adaptation in cereals. Crit Rev Plant Sci. 2008;27(6):377-412. doi: 10.1080/07352680802467736.

43.Maccaferri M, Stefanelli S, Rotondo F, Tuberosa R, Sanguineti MC. Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data. Genome. 2007;50(4):373-84. doi: 10.1139/G06-151.

44.Manifesto MM, Schlatter AR, Hopp HE, Suárez EY, Dubcovsky J. Quantitative evaluation of genetic diversity in wheat germplasm using molecular markers. Crop Sci. 2001;41(3):682-90. doi: 10.2135/cropsci2001.413682x.

45.Marić S, Bolarić S, Martinčić J, Pejić I, Kozumplik V. Genetic diversity of hexaploid wheat cultivars estimated by RAPD markers, morphological traits and coefficients of parentage. Plant Breed. 2004;123(4):366-9. doi: 10.1111/j.1439-0523.2004.00956.x.

46.Schut JW, Qi X, Stam P. Association between relationship measures based on AFLP markers, pedigree data and morphological traits in barley. Theor Appl Genet. 1997;95(7):1161-8. doi: 10.1007/s001220050677.

47.Cupic T, Tucak M, Popovic S, Bolaric S, Grljusic S, Kozumplik V. Genetic diversity of pea (Pisum sativum L.) genotypes assessed by pedigree, morphological and molecular data. J Food Agric Environ. 2009;7(3&4):343-8.

48.Hartings H, Berardo N, Mazzinelli GF, Valoti P, Verderio A, Motto, M. Assessment of genetic diversity and relationships among maize (Zea mays L.) Italian landraces by morphological traits and AFLP profiling. Theorl App Genet. 2008;117(6):831-42. doi: 10.1007/s00122-008-0823-2.

49.van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, de Jesus Sanchez Gonzalez J, et al. Genetic signals of origin, spread, and introgression in a large sample of maize landraces. PNAS. 2011;108(3):1088–92. doi: 10.1073/pnas.1013011108.

引用本文

Mohammed Salah,Shruthi H. Belliappa,Naresh Bomma,Mahesh Pujar,Anilkumar Vemula,Sunil S. Gangurde,Manish K. Pandey,Victor O. Adetimirin,Prakash I. Gangashetty*. Exploring Genetic Diversity and Population Structure in an International Panel of Pigeonpea (Cajanus cajan L. Millsp.) [J]. Crop Breeding, Genetics and Genomics. 2025; 7; (4). - .

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