Genotypic variability and relationships of Sorghum bicolor accessions from Java Island, Indonesia based on IRAP markers
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Abstract. Martiwi INA, Nugroho LH, Daryono BS, Susandarini R. 2020. Genotypic variability and relationships of Sorghum bicolor accessions from Java Island, Indonesia based on IRAP markers. Biodiversitas 21: 5637-5643. Sorghum (Sorghum bicolor (L.) Moench) is a multifunctional crop with high adaptability to various habitats and thus it is important to assess the genotypic variability of this crop species. This study aimed to reveal the genotypic variability and relationships of sorghum accessions using inter-retrotransposon amplified polymorphism (IRAP) molecular markers. Twenty-three sorghum accessions were collected from smallholder farmers in three provinces of Java Island during the 2019 planting season. The IRAP profiles generated using 10 primer combinations produced 233 scorable bands, with degree of polymorphism 75-96.9%. Cluster analysis using the neighbor-joining (NJ) method showed the formation of three groups corresponds to geographic origin of samples. The NJ dendrogram structure indicated high genotypic variability, and was supported by distribution pattern of accessions on the scatterplot constructed using principal coordinate analysis. The grouping of accessions did not correspond to classification of botanical races. Each group recognized from cluster analysis and principal coordinate analysis consisted of various races namely Bicolor, Guinea, Caudatum, and Kaffir. The fact that each group consisted of various botanical races indicated local adaptation and the maintenance of genotypic identity through farmers’ selection in traditional cultivation practices. It could be concluded, therefore, that geographical proximity and the practice of seed exchange between different regions showed considerable influence on the genotypic relationships of sorghum accessions.
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References
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Barnaud A, Deu M, Garine E, McKey D, Joly HI. 2007. Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theor Appl Genet 114: 237–248. doi: 10.1007/s00122-006-0426-8
Berenji J, Dahlberg J, Sikora V, Latkovi D. 2011. Origin, history, morphology, production, improvement, and utilization of broomcorn [Sorghum bicolor (L.) Moench] in Serbia. Econ Bot 65 (2): 190–208. doi: 10.1007/s12231-011-9155-2
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Cheraghi A, Rahmani F, Hassanzadeh-Ghorttapeh A. 2018. IRAP and REMAP based genetic diversity among varieties of Lallemantia iberica. Mol Biol Res Commun 7 (3): 125-132. doi: 10.22099/mbrc.2018.29924.1327
da Silva MJ, Pastina MM, de Souza VF, Schaffert RE, Carneiro PCS, Noda RW, Carneiro JES, Damasceno CMB, Parrella RAC. 2017. Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production. PLoS ONE 12 (8): e0183504. https://doi.org/10.1371/journal.pone.0183504
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https://doi.org/10.1371/journal.pone.0183504
Desmae H, Jordan DR, Godwin ID. 2016. DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces. Afr J Biotechnol 15 (41): 2301-2311. doi: 10.5897/AJB2016.15404
Disasa T, Feyissa T, Admassu B, Paliwal R, Villiers S, Odeny DA. 2016. Molecular evaluation of Ethiopian sweet sorghum germplasm and their contribution to regional breeding programs. Aust J Crop Sci 10 (4): 520-527. doi: 10.21475/AJCS.2016.10.04.P7286X
Farouji AE, Khodayari H, Saeidi H, Rahiminejad MR. 2015. Genetic diversity of diploid Triticum species in Iran assesed using Inter-retroelement amplified Polymorphism (IRAP) markers. Biology 70 (1): 52-60. https://doi.org/10.1515/biolog-2015-0002
Gerrano AS, Labuschagne MT, van Biljon A, Shargie NG. 2014. Genetic variability among sorghum accessions for seed starch and stalk total sugar. Sci Agric 71 (6): 472-479. http://dx.doi.org/10.1590/0103-9016-2013-0322
Ghonaim M, Kalendar R, Barakat H, Elsherif N, Ashry N, Schulman AH. 2020. High?throughput retrotransposon?based genetic diversity of maize germplasm assessment and analysis. Mol Biol Rep 47: 1589–1603. https://doi.org/10.1007/s11033-020-05246-4
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Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4 (1): 9pp. http://palaeo-electronica.org/2001_1/past/issue1_01.htm
Jiang S-Y, Ramachandran S. 2013. Genome-wide survey and comparative analysis of LTR retrotransposon and their captured genes in rice and Sorghum. PLoS ONE 8 (7): e71118. https://doi.org/10.1371/journal.pone.0071118
Kalendar R, Grob T, Regina M, Suoniemi A, Schulman AH. 1999. IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98: 704-711.
Kalendar R. Taskanen J, Imonen S, Nevo E, Schulman AH. 2000. Genom evolution of wild barley (Hordeum spotaneum) by BARE-1 retrotransoposon dynamics in response to sharp microclimate divergence. Proc Natl Acad Sci USA 97: 6603-6607.
Karimi A, Saeidi H. 2016. Genetic diversity of Sorghum halepense (L.) Pers. in Iran as revealed by IRAP markers. Plant Genet Resour 14 (2): 132–141. doi:10.1017/S1479262115000167
Kebbede WY. 2020. Genetic Variability and Divergence in Sorghum: Review. Int J Res Stud Agric Sci 6 (5): 11-20. doi: http://dx.doi.org/10.20431/2454-6224.0605002
Khalsa SDK. 2013. Genetic structure and diversity of Sorghum bicolor at three geographical scales in Africa. Master of Science Thesis, Department of Biology, University of Oslo.
Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT , Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Morris GP. 2015. Genome-environment associations in sorghum landraces predict adaptive traits. Sci Adv 2015;1:e1400218. doi: 10.1126/sciadv.1400218
Madhusudhana R, Balakrishna D, Rajendrakumar P, Seetharama N, Patil JV. 2012. Molecular characterization and assessment of genetic diversity of sorghum inbred lines. Afr J Biotechnol 11 (90): 15626-15635. doi: 10.5897/AJB12.321
Mansour A. 2008. Utilization of genomics retrotranposon as cladistic makers. J Cell Mol Biol 7: 17-28.
Martiwi INA, Nugroho LH, Daryono BS, Susandarini R. 2020. Morphological variability and taxonomic relationship of Sorghum bicolor (L.) Moench accessions based on qualitative characters. Annu Res Rev Biol 35 (6): 40-52. doi: 10.9734/ARRB/2020/v35i630234
Mumtaz A, Hussain D, Saeed M, Arshad M, Yousaf MI. 2018. Estimation of genetic diversity in sorghum genotypes of Pakistan. J Natn Sci Foundation Sri Lanka 46 (3): 271-280. http://dx.doi.org/10.4038/jnsfsr.v46i3.8479
Ng’uni D, Geleta M, M Fatih M, Bryngelsson T. 2010. Phylogenetic analysis of the genus Sorghum based on combined sequence data from cpDNA regions and ITS generate well-supported trees with two major lineages. Ann Bot 105: 471–480. doi:10.1093/aob/mcp305
Salih SA, Herslman L, Labuschange MT, Mohammed CAH. 2016. Assessment of genetic diversity of sorghum [Sorghum bicolor (L.) Moench] germplasm in east and central Africa. World J Biotechnol 1 (3): 113-120.
Sant’Anna IC, Silva GN, Carneiro VQ, Pontes DS, Nascimento M, Cruz CD. 2020. of projection of distance techniques for genetic diversity studies. Acta Sci Agron 42: e42483 (on-line journal). doi: 10.4025/actasciagron.v42i1.42483
Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P. 2000. A Contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10: 908–915.
Singh S, Nandha PS, Singh J. 2017. Transposon-based genetic diversity assessment in wild and cultivated barley. Crop J 5: 296-304. http://dx.doi.org/10.1016/j.cj.2017.01.003
Tagimanova DS, Novakovskaya AP, Uvashov AO, Khapilina ON, Kalendar RN. 2015. Use of retrotransposon markers for analysing the genetic diversity of wild emmer wheat (Triticum dicoccoides). Biotechnol Theory Pract 4: 28-37. doi: 10.11134/btp.4.2015.4
Tesfaye K. 2017. Genetic diversity study of sorghum (Sorghum bicolor (L.) Moenc) genotypes, Ethiopia. Acta Univ Sapientiae Agric Environ 9: 44-54. doi: 10.1515/ausae-2017-0004
Teo CH, Tan SH, Ho CL, Faridah QZ, Othman YR, Heslop-Harrison JS, Kalendar R, Schulman AH. 2005. Genome constitution and classification using retrotransposon- based markers in the orphan crop banana. J Plant Biol 48 (1): 96-105.
Vigouroux ,Y Barnaud A, Scarcelli N, Thuillet A-C. 2011. Biodiversity, evolution and adaptation of cultivated crops. C. R. Biol 334: 450–457. doi:10.1016/j.crvi.2011.03.003
Vuorinen AL, Kalendar R, Fahima T, Korpelainen H, Nevo E, Schulman AH. 2018. Retrotransposon-based genetic diversity assessment in wild emmer wheat (Triticum turgidum ssp. dicoccoides). Agronomy 8: 107. doi:10.3390/agronomy8070107
Alhajturki D, Al Jamali M, Kanbar A. 2011. Genetic variation of sorghum (Sorghum bicolor L. Moench) varieties assessed by ISSR markers. Adv Environ Biol 5 (11): 3504-3510.
Badigannavar A, Teme N, de Oliveira AC, Li G, Vaksmann M, Viana VE, Ganapathi TR, Sarsu F. 2018. Physiological, genetic and molecular basis of drought resilience in sorghum [Sorghum bicolor (L.) Moench]. Ind J Plant Physiol 23 (4): 670–688. https://doi.org/10.1007/s40502-018-0416-2
Barnaud A, Deu M, Garine E, McKey D, Joly HI. 2007. Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces. Theor Appl Genet 114: 237–248. doi: 10.1007/s00122-006-0426-8
Berenji J, Dahlberg J, Sikora V, Latkovi D. 2011. Origin, history, morphology, production, improvement, and utilization of broomcorn [Sorghum bicolor (L.) Moench] in Serbia. Econ Bot 65 (2): 190–208. doi: 10.1007/s12231-011-9155-2
Castelo J. S. Branco, Eduardo A. Vieira, Gaspar Malone, Mauricio M. Kopp, Emilia Malone, Albina Bernardes, Claudete C. Mistura, Fernando I.F. Carvalho, Costa A. Oliveira. 2007. IRAP and REMAP assessments of genetic similarity in rice. J Appl Genet 48 (2): 107–113.
Chavan SK, Mahajan RC, Fatak SU. 2010. Genetic variability studies in sorghum. Karnataka J Agric Sci 23 (2): 322-323.
Cheraghi A, Rahmani F, Hassanzadeh-Ghorttapeh A. 2018. IRAP and REMAP based genetic diversity among varieties of Lallemantia iberica. Mol Biol Res Commun 7 (3): 125-132. doi: 10.22099/mbrc.2018.29924.1327
da Silva MJ, Pastina MM, de Souza VF, Schaffert RE, Carneiro PCS, Noda RW, Carneiro JES, Damasceno CMB, Parrella RAC. 2017. Phenotypic and molecular characterization of sweet sorghum accessions for bioenergy production. PLoS ONE 12 (8): e0183504. https://doi.org/10.1371/journal.pone.0183504
Dahlberg J, Berenji J, Sikora V, Latkovi? D. 2011. Assessing sorghum [Sorghum bicolor (L) Moench] germplasm for new traits: food, fuels & unique uses. Maydica 56-1750: 85-92.
https://doi.org/10.1371/journal.pone.0183504
Desmae H, Jordan DR, Godwin ID. 2016. DNA markers reveal genetic structure and localized diversity of Ethiopian sorghum landraces. Afr J Biotechnol 15 (41): 2301-2311. doi: 10.5897/AJB2016.15404
Disasa T, Feyissa T, Admassu B, Paliwal R, Villiers S, Odeny DA. 2016. Molecular evaluation of Ethiopian sweet sorghum germplasm and their contribution to regional breeding programs. Aust J Crop Sci 10 (4): 520-527. doi: 10.21475/AJCS.2016.10.04.P7286X
Farouji AE, Khodayari H, Saeidi H, Rahiminejad MR. 2015. Genetic diversity of diploid Triticum species in Iran assesed using Inter-retroelement amplified Polymorphism (IRAP) markers. Biology 70 (1): 52-60. https://doi.org/10.1515/biolog-2015-0002
Gerrano AS, Labuschagne MT, van Biljon A, Shargie NG. 2014. Genetic variability among sorghum accessions for seed starch and stalk total sugar. Sci Agric 71 (6): 472-479. http://dx.doi.org/10.1590/0103-9016-2013-0322
Ghonaim M, Kalendar R, Barakat H, Elsherif N, Ashry N, Schulman AH. 2020. High?throughput retrotransposon?based genetic diversity of maize germplasm assessment and analysis. Mol Biol Rep 47: 1589–1603. https://doi.org/10.1007/s11033-020-05246-4
Gozukirmizi N, Yilmaz S, Marakli S, Temel A. 2015. Retrotransposon-based molecular markers; Tools for variation analysis in plants. In: Ksenija Taški-Ajdukovi? (Ed.). Applications of Molecular Markers in Plant Genome Analysis and Breeding. pp: 19-45. Research Signpost, Kerala, India.
Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4 (1): 9pp. http://palaeo-electronica.org/2001_1/past/issue1_01.htm
Jiang S-Y, Ramachandran S. 2013. Genome-wide survey and comparative analysis of LTR retrotransposon and their captured genes in rice and Sorghum. PLoS ONE 8 (7): e71118. https://doi.org/10.1371/journal.pone.0071118
Kalendar R, Grob T, Regina M, Suoniemi A, Schulman AH. 1999. IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98: 704-711.
Kalendar R. Taskanen J, Imonen S, Nevo E, Schulman AH. 2000. Genom evolution of wild barley (Hordeum spotaneum) by BARE-1 retrotransoposon dynamics in response to sharp microclimate divergence. Proc Natl Acad Sci USA 97: 6603-6607.
Karimi A, Saeidi H. 2016. Genetic diversity of Sorghum halepense (L.) Pers. in Iran as revealed by IRAP markers. Plant Genet Resour 14 (2): 132–141. doi:10.1017/S1479262115000167
Kebbede WY. 2020. Genetic Variability and Divergence in Sorghum: Review. Int J Res Stud Agric Sci 6 (5): 11-20. doi: http://dx.doi.org/10.20431/2454-6224.0605002
Khalsa SDK. 2013. Genetic structure and diversity of Sorghum bicolor at three geographical scales in Africa. Master of Science Thesis, Department of Biology, University of Oslo.
Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT , Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Morris GP. 2015. Genome-environment associations in sorghum landraces predict adaptive traits. Sci Adv 2015;1:e1400218. doi: 10.1126/sciadv.1400218
Madhusudhana R, Balakrishna D, Rajendrakumar P, Seetharama N, Patil JV. 2012. Molecular characterization and assessment of genetic diversity of sorghum inbred lines. Afr J Biotechnol 11 (90): 15626-15635. doi: 10.5897/AJB12.321
Mansour A. 2008. Utilization of genomics retrotranposon as cladistic makers. J Cell Mol Biol 7: 17-28.
Martiwi INA, Nugroho LH, Daryono BS, Susandarini R. 2020. Morphological variability and taxonomic relationship of Sorghum bicolor (L.) Moench accessions based on qualitative characters. Annu Res Rev Biol 35 (6): 40-52. doi: 10.9734/ARRB/2020/v35i630234
Mumtaz A, Hussain D, Saeed M, Arshad M, Yousaf MI. 2018. Estimation of genetic diversity in sorghum genotypes of Pakistan. J Natn Sci Foundation Sri Lanka 46 (3): 271-280. http://dx.doi.org/10.4038/jnsfsr.v46i3.8479
Ng’uni D, Geleta M, M Fatih M, Bryngelsson T. 2010. Phylogenetic analysis of the genus Sorghum based on combined sequence data from cpDNA regions and ITS generate well-supported trees with two major lineages. Ann Bot 105: 471–480. doi:10.1093/aob/mcp305
Salih SA, Herslman L, Labuschange MT, Mohammed CAH. 2016. Assessment of genetic diversity of sorghum [Sorghum bicolor (L.) Moench] germplasm in east and central Africa. World J Biotechnol 1 (3): 113-120.
Sant’Anna IC, Silva GN, Carneiro VQ, Pontes DS, Nascimento M, Cruz CD. 2020. of projection of distance techniques for genetic diversity studies. Acta Sci Agron 42: e42483 (on-line journal). doi: 10.4025/actasciagron.v42i1.42483
Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P. 2000. A Contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10: 908–915.
Singh S, Nandha PS, Singh J. 2017. Transposon-based genetic diversity assessment in wild and cultivated barley. Crop J 5: 296-304. http://dx.doi.org/10.1016/j.cj.2017.01.003
Tagimanova DS, Novakovskaya AP, Uvashov AO, Khapilina ON, Kalendar RN. 2015. Use of retrotransposon markers for analysing the genetic diversity of wild emmer wheat (Triticum dicoccoides). Biotechnol Theory Pract 4: 28-37. doi: 10.11134/btp.4.2015.4
Tesfaye K. 2017. Genetic diversity study of sorghum (Sorghum bicolor (L.) Moenc) genotypes, Ethiopia. Acta Univ Sapientiae Agric Environ 9: 44-54. doi: 10.1515/ausae-2017-0004
Teo CH, Tan SH, Ho CL, Faridah QZ, Othman YR, Heslop-Harrison JS, Kalendar R, Schulman AH. 2005. Genome constitution and classification using retrotransposon- based markers in the orphan crop banana. J Plant Biol 48 (1): 96-105.
Vigouroux ,Y Barnaud A, Scarcelli N, Thuillet A-C. 2011. Biodiversity, evolution and adaptation of cultivated crops. C. R. Biol 334: 450–457. doi:10.1016/j.crvi.2011.03.003
Vuorinen AL, Kalendar R, Fahima T, Korpelainen H, Nevo E, Schulman AH. 2018. Retrotransposon-based genetic diversity assessment in wild emmer wheat (Triticum turgidum ssp. dicoccoides). Agronomy 8: 107. doi:10.3390/agronomy8070107
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