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Establishing core collections for enhanced use of germplasm in crop improvement

Year 2015, Volume: 1 Issue: 1, 1 - 12, 01.01.2015

Abstract

Plant genetic resources are the basic raw materials and their use in breeding is the most sustainable way to conserve biodiversity. Low use of germplasm in crop improvement programs has resulted large gap between the number of germplasm preserved in genebanks and the number of germplasm used in crop breeding across the globe. Breeders are reluctant to use germplasm largely either due to lack of reliable information on economic traits besides linkage drag or due to breakdown of co-adapted gene complexes, which may prolong cultivar development time. The reduced subsets, representing diversity in the germplasm collection of a given species preserved in genebank, in the form of core or mini core collections are the ideal genetic resources for discovering new sources of variations for use in crop improvement programs. Two decades of research at ICRISAT has led to the establishment of core and mini core collections and their subsequent evaluations has resulted in identification of new sources of variations, for example, resistance to abiotic and/or biotic stresses in chickpea, groundnut, pigeonpea, pearl millet, sorghum, finger millet and foxtail millet. Likewise, a number of nutritionally dense (high protein, Ca, Fe and Zn) germplasm have been identified in finger millet, foxtail millet, groundnut, pearl millet, and sorghum. A few groundnut germplasm with improved oil quality, as determined by variation in oleic and linoleic fatty acids, were also identified. Many of these germplasm were agronomically at par or even superior over controls and showed specific and wide adaptation. The identified sources may be used in genomics and breeding to broaden the cultigen’s genepool in these crops

References

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  • FAO (2010). The second report on the state of the world’s Plant Genetic Resources for food and agriculture. http://www.fao.org/docrep/013/i1500e/i1500e. pdf.
  • Fernando WMU, Hill JE, Zello GA, Tyler RT, Dahl WJ and Van Kessel AG (2010). Diets supplemented with chickpea or its main oligosaccharide component raffinose modify fecal microbial composition in healthy adults. Benef. Microbes 1:197-207.
  • Frankel OH (1984). Genetic perspective of germplasm collection. In: Genetic manipulations: impact on man and society, Arber W, Limensee K, Peacock WJ and Stralinger P (eds.), Cambridge University Press, Cambridge, pp: 61-170.
  • Gaur PM, Jukanti AK, Samineni S, Chaturvedi SK, Singh S, Tripathi S, Singh I, Singh G, Das TK, Aski M, Mishra N, Nadarajan N and Gowda CLL (2013). Large variability in chickpea for tolerance to herbicides imazethapyr and metribuzin. Agronomy 3:524-536.
  • Generation Challenge Program Project abstracts (2008). Generation Challenge Program: Cultivating plant diversity for the resource poor. (Abstract). pp. 47- 50 and 64-66. Glaszmann JC, Kilian B, Upadhyaya HD and Varshney RK (2010). Accessing genetic diversity for crop improvement. Curr. Opin. Plant Biol. 13:167-173.
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  • Grenier C, Hamon P and Bramel-Cox PJ (2001). Core collection of sorghum: II. Comparison of three random sampling strategies. Crop Sci. 41:241- 246.
  • Hamilton JP and Buell CR (2012). Advances in plant genome sequencing. Plant J. 70:177-190.
  • Kiran Babu T, Thakur RP, Upadhyaya HD, Reddy PN, Sharma R, Girish A and Sarma NDRK (2013). Resistance to blast (Magnaporthe grisea) in a mini core collection of finger millet germplasm. Eur. J. Plant Pathol. 135:299-311.
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  • Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc. Natl. Acad. Sci. (USA) 110:453-458. Ortiz R, Ruiz-Tapia EN and Mujica-Sanchez A (1998). Sampling strategy for a core collection of Peruvian quinova germplasm. Theor. Appl. Genet. 96:475-483.
  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten, U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Beller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Rahman M, Ware D, Westhoff P, Mayer KFL, Messing J and Rokhsar DS (2009). The Sorghum bicolor genome and the diversification of grasses. Nature 457:551- 556.
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Year 2015, Volume: 1 Issue: 1, 1 - 12, 01.01.2015

Abstract

References

  • Billot C, Ramu P, Bouchet S, Chantereau J, Deu M, Gardes L, Noyer J-L, Rami J-F, Rivallan R, Li Y, Lu P, Wang T, Folkertsma RT, Arnaud E, Upadhyaya HD, Glaszmann J-C and Hash CT (2013). Massive sorghum collection genotyped with SSR markers to enhance use of global genetic resources. PLoS ONE 8: e59714.
  • Dwivedi SL, Upadhyaya HD and Gowda CLL (2009). Approaches to enhance the value of genetic resources in crop improvement. The FAO Regional Project “Capacity building and enhanced regional collaboration for the conservation and sustainable use of plant genetic resources in Asia”. (http:// www.fao.org/docrep/014/am265e00.pdf).
  • FAO (2010). The second report on the state of the world’s Plant Genetic Resources for food and agriculture. http://www.fao.org/docrep/013/i1500e/i1500e. pdf.
  • Fernando WMU, Hill JE, Zello GA, Tyler RT, Dahl WJ and Van Kessel AG (2010). Diets supplemented with chickpea or its main oligosaccharide component raffinose modify fecal microbial composition in healthy adults. Benef. Microbes 1:197-207.
  • Frankel OH (1984). Genetic perspective of germplasm collection. In: Genetic manipulations: impact on man and society, Arber W, Limensee K, Peacock WJ and Stralinger P (eds.), Cambridge University Press, Cambridge, pp: 61-170.
  • Gaur PM, Jukanti AK, Samineni S, Chaturvedi SK, Singh S, Tripathi S, Singh I, Singh G, Das TK, Aski M, Mishra N, Nadarajan N and Gowda CLL (2013). Large variability in chickpea for tolerance to herbicides imazethapyr and metribuzin. Agronomy 3:524-536.
  • Generation Challenge Program Project abstracts (2008). Generation Challenge Program: Cultivating plant diversity for the resource poor. (Abstract). pp. 47- 50 and 64-66. Glaszmann JC, Kilian B, Upadhyaya HD and Varshney RK (2010). Accessing genetic diversity for crop improvement. Curr. Opin. Plant Biol. 13:167-173.
  • Gowda CLL, Upadhyaya HD, Dronavalli N and Singh S (2011).Identification of large-seeded highyielding stable kabuli chickpea germplasm lines for use in crop improvement. Crop Sci. 51:198- 209.
  • Grenier C, Hamon P and Bramel-Cox PJ (2001). Core collection of sorghum: II. Comparison of three random sampling strategies. Crop Sci. 41:241- 246.
  • Hamilton JP and Buell CR (2012). Advances in plant genome sequencing. Plant J. 70:177-190.
  • Kiran Babu T, Thakur RP, Upadhyaya HD, Reddy PN, Sharma R, Girish A and Sarma NDRK (2013). Resistance to blast (Magnaporthe grisea) in a mini core collection of finger millet germplasm. Eur. J. Plant Pathol. 135:299-311.
  • Krishnamurthy L, Kashiwagi J, Tobita S, Osamu I, Upadhyaya HD, Gowda CLL, Gaur PM, Sheshshayee MS, Singh S, Vadez V and Varshney RK (2013a). Variation in carbon isotope discrimination and its relationship with harvest index in the reference collection of chickpea germplasm. Funct. Plant Biol. 40:1350-1361.
  • Krishnamurthy L, Kashiwagi J, Upadhyaya HD, Gowda CLL, Gaur PM, Singh S, Purushothaman R and Varshney RK (2013b). Partitioning coefficient – a trait that contributes to drought tolerance in chickpea. Field Crops Res. 149:354-365.
  • Krishnamurthy L, Upadhyaya HD, Saxena KB and Vadez V (2012). Variation for temporary water logging response within the mini core pigeonpea germplasm. J. Agric. Sci. 150: 357-364.
  • Krishnamurthy L, Upadhyaya HD, Purushothaman R, Gowda CLL, Kashiwagi J, Dwivedi SL, Singh S and Vadez V (2014a). The extent of variation in salinity tolerance of the mini core collection of finger millet (Eleusine coracana L. Gaertn.) germplasm. Plant Sci. 227:51-59.
  • Krishnamurthy L, Upadhyaya HD, Gowda CLL, Kashiwagi J, Purushothaman R, Singh S and Vadez V (2014b). Large variation for salinity tolerance in the core collection of foxtail millet (Setaria italica (L.) P. Beauv.) germplasm. Crop Pasture Sci. 65:353-361.
  • Kumar AA, Reddy BVS, Ramaian B, Reddy PS, Sahrawat KL and Upadhyaya HD (2009). Genetic variability and plant character association of grain Fe and Zn in selected core collection accessions of sorghum germplasm and breeding lines. eSAT J. 7.
  • Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS and Wang J (2010). Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genetics 42:1027-1030.
  • McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke J M, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, RossIbarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel
  • D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P and Zamir D (2013). Agriculture: Feeding the future. Nature 499:23-24.
  • Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES and Krecovich S (2013).
  • Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc. Natl. Acad. Sci. (USA) 110:453-458. Ortiz R, Ruiz-Tapia EN and Mujica-Sanchez A (1998). Sampling strategy for a core collection of Peruvian quinova germplasm. Theor. Appl. Genet. 96:475-483.
  • Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten, U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Beller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Rahman M, Ware D, Westhoff P, Mayer KFL, Messing J and Rokhsar DS (2009). The Sorghum bicolor genome and the diversification of grasses. Nature 457:551- 556.
  • Rathinavel K, Manickam S and Sabesh M (2005). Training manual on DUS test in cotton with reference to PVV and FR legislation. Reddy LJ, Upadhyaya HD, Gowda CLL and Singh S (2005). Development of core collection in pigeonpea [Cajanus cajan (L.) Millspaugh] using geographic and qualitative morphological descriptors. Genet. Resour. Crop Evol. 52:1049- 1056.
  • Sharma R, Rao VP, Upadhyaya HD, Reddy VG and Thakur RP (2010). Resistance to grain mold a n d downy mildew in a minicore collection of sorghum germplasm. Plant Dis. 94: 439-444.
  • Sharma M, Rathore A, Mangala UN, Ghosh R, Sharma S, Upadhyaya HD and Pande S (2012a). New sources of resistance to fusarium wilt and sterility mosaic in a mini core collection of pigeonpea germplasm. Eur. J. Plant Pathol. 133:707-714.
  • Sharma R, Upadhyaya HD, Manjunatha SV, Rao VP and Thakur RP (2012b). Resistance to foliar diseases in a mini core collection of sorghum germplasm. Plant Dis. 96:1629-1633.
  • Sharma R, Girish AG, Upadhyaya HD, Humayun P, Talluri KB, Panduranga Rao V and Thakur RP (2013a). Identification of blast resistance in a core collection of foxtail millet germplasm. Plant Dis. 98:519-524
  • Sharma R, Upadhyaya HD, Manjunatha SV, Rai KN, Gupta SK and Thankur RP (2013b). Pathogenic variation in the pearl millet blast pathogen Magnaporthe grisea and identification of resistance to diverse pathotypes. Plant Dis. 97:189-195.
  • Smith SC, Choy R, Johnson SK, Hall RS, Wildeboer-Veloo ACM and Welling GW (2006). Lupin kernel fiber consumption modifies fecal microbiota in healthy men as determined by rRNA gene fluorescent in situ hybridization. Eur. J. Nutr. 45:335-341.
  • Upadhyaya HD, Bramel PJ, Ortiz R and Singh S (2002). Developing a mini core of peanut for utilization of genetic resources. Crop Sci. 42:2150-2156.
  • Upadhyaya HD, Bramel PJ and Singh S (2001). Development of a chickpea core subset using geographic distribution and quantitative traits. Crop Sci. 41:206-210.
  • Upadhyaya HD, Dronavalli N, Singh S and Dwivedi SL (2012a). Variability and stability for kernel iron and zinc contents in the ICRISAT mini core collection of peanut. Crop Sci. 52:2628-2637.
  • Upadhyaya HD, Mukri G, Nadaf HL and Singh S (2012b). Variability and stability analysis for nutritional traits in the mini core collection of peanut. Crop Sci. 52:168–178.
  • Upadhyaya HD, Wang Y-H, Sharma S, Singh S and Hasentstein KH (2012c). SSR markers linked to kernel weight and tiller number in sorghum identified by association mapping. Euphytica 187:401-410.
  • Upadhyaya HD, Dronavalli N, Dwivedi SL, Kashiwagi K, Krishnamurthy L, Pande S, Sharma HC, Vadez V, Singh S, Varshney RK and Gowda CLL (2013a). Mini core collection as a resource to identifying new sources of variation for use in chickpea breeding and genomics. Crop Sci. 53:2506-2517.
  • Upadhyaya HD, Wang Y-H, Gowda CLL and Sharma S (2013b) Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection. Theor. Appl. Genet. 126:2003-2015.
  • Upadhyaya HD, Wang Y-H, Sharma R and Sharma S (2013c). Identification of genetic markers linked to anthracnose resistance in sorghum using association analysis. Theor. Appl. Genet. 126:1649-1657.
  • Upadhyaya HD, Wang Y-H, Sharma R and Sharma S (2013d). SNP markers linked to leaf rust and grain mold resistance in sorghum. Mol. Breed. 32:451- 462.
  • Upadhyaya HD, Dwivedi SL, Vadez V, Hamidou F, Singh S, Varshney RK and Liao B (2014a). Multiple resistance and nutritionally dense germplasm identified from mini core collection in groundnut. Crop Sci. 54:679-693.
  • Upadhyaya HD, Dwivedi SL, Ramu P, Singh SK and Singh S (2014b). Effect of post - flowering drought on genetic variability for stalk sugar content in sorghum mini core collection. Crop Sci. 54:2120- 2130.
  • Upadhyaya HD, Dwivedi SL, Singh SK, Singh S, Vetriventhan M and Sharma S (2014c). Forming core collections in barnyard, kodo, and little millets using morphoagronomic descriptors. Crop Sci. 54:2673-2682.
  • Upadhyaya HD, Dwivedi SL, Baun M, Varshney RK, Udupa SM, Gowda CLL, Hoisington D and Singh S (2008a). Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biol. 8:106.
  • Upadhyaya HD, Pundir RPS, Gowda CLL, Reddy VG and Singh S (2008b). Establishing a core collection of foxtail millet to enhance the utilization of germplasm of an underutilized crop. Plant Genet. Resour. 7:177-184.
  • Upadhyaya HD, Reddy LJ, Gowda CLL, Reddy KN and Singh S (2006a). Development of a mini core subset for enhanced and diversified utilization of pigeonpea germplasm resources. Crop Sci. 46:2127-2132.
  • Upadhyaya HD, Gowda CLL, Pundir RPS, Reddy VG and Singh S (2006b). Development of core subset of finger millet germplasm using geographical origin and data on 14 quantitative traits. Genet. Resour. Crop Evol. 53:679-685.
  • Upadhyaya HD, Reddy LJ, Gowda CLL, Singh S (2006c). Identification of diverse groundnut germplasm: Sources of early maturity in a core collection. Field Crops Res. 97:261-271.
  • Upadhyaya HD, Pundir RPS, Dwivedi SL, Gowda CLL (2009a). Mini core collections for e f f i c i e n t utilization of plant genetic resources in crop improvement programs. Inf. Bull. no. 78. pp. 52.
  • Upadhyaya HD, Gowda CLL, Reddy KN and Singh S (2009b). Augmenting the pearl millet core collection for enhancing germplasm utilization in crop improvement. Crop Sci. 49: 573-580.
  • Upadhyaya HD, Pundir RPS, Dwivedi SL, Gowda CLL, Reddy VG and Singh S (2009c). Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci. 49:1769- 1780.
  • Upadhyaya HD and R Ortiz (2001). A mini core subset for capturing diversity and promoting utilization of chickpea genetic resources in crop improvement. Theor. Appl. Genet. 102: 1292-1298.
  • Upadhyaya HD, R Ortiz, Bramel PJ and Singh S (2003). Development of a groundnut core collection using taxonomical, geographical and morphological descriptors. Genet. Resour. Crop Evol. 50:139- 148.
  • Upadhyaya HD, Salimath PM, Gowda CLL and Singh S (2007). New early-maturing germplasm lines for utilization in chickpea improvement. Euphytica 157:195-208.
  • Upadhyaya HD, Sarma NDRK, Ravishankar CR, Albrecht T, Narsimhudu Y, Singh SK, Varshney SK, Reddy VG, Singh S, Dwivedi SL, Wanyera N, Oduori COA, Mgonja MA, Kisandu DB, Parzies HK and Gowda CLL (2010). Developing a mini core collection in finger millet using multilocation data. Crop Sci. 50:1924-1931.
  • Upadhyaya, HD, Yadav D, Reddy KN, Gowda CLL and Singh S (2011a). Development of pearl millet mini core collection for enhanced utilization of germplasm. Crop Sci. 51:227-223.
  • Upadhyaya HD, Ravishankar CR, Narsimhudu Y, Sarma NDRK, Singh SK, Varshney SK, Reddy VG, Singh S, Parzies HK, Dwivedi SL, Nadaf HL, Sahrawat KL and Gowda CLL (2011b). Identification of trait-specific germplasm and developing a mini core collection for efficient use of foxtail millet genetic resources in crop improvement. Field Crops Res. 124:459-467.
  • Upadhyaya HD, Sharma S, Gowda CLL, Reddy VG and Singh S (2011c). Developing proso millet (Panicum miliaceum L.) core collection using geographic and morpho-agronomic data. Crop Pasture Sci. 62:383-389.
  • Upadhyaya HD, Ramesh S, Sharma S, Singh SK, Varshney SK, Sarma N D R K, Ravishankar C R, Narasimhudu Y, Reddy VG, Sahrawat KL, Dhalalakshmi TN, Mgonja MA, Parzies HK, Gowda CLL and Singh S (2011d). Genetic diversity for grain nutrients in a core collection of finger millet (Eleusine coracana (L.) Gaertn.) germplasm. Field Crops Res. 121: 42-52.
  • Upadhyaya HD, Thudi M, Dronavali N, Gujaria N, Singh S, Sharma S and Varshney RK (2011e). Genomic tools and germplasm diversity for chickpea improvement. Plant Genetic Resources 9: 45-58.
  • Vadez V, Krishnamurthy L, Hash CT, Upadhyaya HD and Borrell AK (2011). Yield, transpiration efficiency, and water-use variations and their relationships in the sorghum reference collection. Crop Pasture Sci. 62:645-655.
  • Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter, JA, Donoghue MTA, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, Wu W, Upadhyaya HD, Yang S-P, Shah T, Saxena KB, Michael T, McCombie WR, Yang B, Zhang G, Yang H, Wang J, Spillane C, Cook DR, May GD, Xu X and Jackson SA (2012). Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology 30: 83-89.
  • Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar’an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M-C, Thudi M, Gowda CLL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J and Cook DR (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31: 240-246
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There are 65 citations in total.

Details

Other ID JA35UM44MK
Journal Section Articles
Authors

Hari D. Upahyaya This is me

Publication Date January 1, 2015
Published in Issue Year 2015 Volume: 1 Issue: 1

Cite

APA Upahyaya, H. D. (2015). Establishing core collections for enhanced use of germplasm in crop improvement. Ekin Journal of Crop Breeding and Genetics, 1(1), 1-12.
AMA Upahyaya HD. Establishing core collections for enhanced use of germplasm in crop improvement. Ekin Journal. January 2015;1(1):1-12.
Chicago Upahyaya, Hari D. “Establishing Core Collections for Enhanced Use of Germplasm in Crop Improvement”. Ekin Journal of Crop Breeding and Genetics 1, no. 1 (January 2015): 1-12.
EndNote Upahyaya HD (January 1, 2015) Establishing core collections for enhanced use of germplasm in crop improvement. Ekin Journal of Crop Breeding and Genetics 1 1 1–12.
IEEE H. D. Upahyaya, “Establishing core collections for enhanced use of germplasm in crop improvement”, Ekin Journal, vol. 1, no. 1, pp. 1–12, 2015.
ISNAD Upahyaya, Hari D. “Establishing Core Collections for Enhanced Use of Germplasm in Crop Improvement”. Ekin Journal of Crop Breeding and Genetics 1/1 (January 2015), 1-12.
JAMA Upahyaya HD. Establishing core collections for enhanced use of germplasm in crop improvement. Ekin Journal. 2015;1:1–12.
MLA Upahyaya, Hari D. “Establishing Core Collections for Enhanced Use of Germplasm in Crop Improvement”. Ekin Journal of Crop Breeding and Genetics, vol. 1, no. 1, 2015, pp. 1-12.
Vancouver Upahyaya HD. Establishing core collections for enhanced use of germplasm in crop improvement. Ekin Journal. 2015;1(1):1-12.