Skip to main content
SpringerLink
Log in

Trait phenotyping and molecular marker characterization of barley (Hordeum vulgare L.) germplasm from Western Himalayas

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

Barley (Hordeum vulgare L.) is one of the principal cereal crops grown in Western-Himalayas of India. A set of 105 barley genotypes including 38 two-rowed and 67 six-rowed genotypes were phenotyped for 10 important quantitative traits. The analysis of trait data of pre-harvest sprouting tolerance (PHST), growth, yield and yield contributing traits revealed significant variation in the germplasm and led to the identification of promising candidate genotypes for all the traits. In addition, a set of 96 barley genotypes were subjected to molecular characterization using 14 unlinked SSR markers (7 random and 7 genic SSR markers). The analysis of SSR marker data revealed a total of 67 alleles (range 2 to 8) with an average of 4.78 alleles/locus. While analyzing the data separately for random and genic SSR markers, it was observed that genic SSR markers are slightly less diverse (4.71 alleles/locus) than random genomic SSR markers (4.85 alleles/locus). A set of three markers including two random (XBmac156 and XBmag378) and one genic (XGbm1221) SSR marker detecting 7–8 alleles were found most polymorphic/informative markers for the study of allelic diversity in barley. The clustering of 96 genotypes based on genotypic data categorized all the genotypes into three broad clusters, sub- clusters and sub-sub clusters. The genotypes clustered in three sub-clusters did not show any trait-specific relationship with each other. The overall result of genotypic data analysis indicated moderate-level of genetic diversity in the 96 barley genotypes. The diverse and most promising genotypes identified for different traits during the present study could prove useful in future barley breeding programs worldwide.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Abebe T, Melmaiee K, Berg V, Wise RP (2010) Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed. Funct Integr Genomics 10(2):191–205

    CAS  PubMed  Google Scholar 

  • Assefa A, Labuschagne MT (2004) Phenotypic variation in barley (Hordeum vulgare L.) landraces from north Shewa in Ethiopia. Biodivers Conserv 13(8):1441–1451

  • Baik BK, Ullrich SE (2008) Barley for food: characteristics, improvement, and renewed interest. J Cereal Sci 48:233–242

    CAS  Google Scholar 

  • Benmahammed L, Bouzerzour H, Benmahammed A, Mimouni H (2011) Assessment of the phenotypic variation with in two- and six-rowed barley (Hordeum Vulgare L.) breeding lines grown under semi-arid conditions. Adv Environ Biol 5(7):1454–1461

  • Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Philos Trans R Soc Lond B 274:227–274

    CAS  Google Scholar 

  • Bensemane L, Bouzerzour H, Benmahammed A, Mimouni H (2011) Assessment of the phenotypic variation within two-and six-rowed barley (Hordeum vulgare L.) breeding lines grown under semi-arid conditions. Adv Environ Biol 1454–1461

  • Bewley JD, Black M (1994) Seeds: physiology of development and germination, vol 2. Plenum Press, New York

    Google Scholar 

  • Blum A (1985) Photosynthesis and transpiration in leaves and ears of wheat and barley varieties. J Exp Bot 36:432–440

    Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314

    CAS  PubMed  PubMed Central  Google Scholar 

  • Brbaklic L, Trkulja D, Mikic S, Mirosavljevic M, Momcilovic V, Dudic B, Procházková L, Acin V (2021) Genetic diversity and population structure of Serbian barley (Hordeum vulgare L.) collection during a 40-year long breeding period. Agronomy 11:118

  • Choudhary N, Hamid A, Singh B, Khandy I, Sofi PA, Bhat MA, Mir RR (2018a) Insight into the origin of common bean (Phaseolus vulgaris L.) grown in the state of Jammu and Kashmir of north-western Himalayas. Genet Resour Crop Evol 65(3):963–977

  • Choudhary N, Bawa V, Paliwal R, Singh B, Bhat MA, Mir JI et al (2018b) Gene/QTL discovery for Anthracnose in common bean (Phaseolus vulgaris L.) from North-western Himalayas. PLoS ONE 13(2):e0191700

  • Chen ZW, Lu RJ, Zou L, Gao RH, Huang JH (2012) Genetic diversity analysis of barley landraces and cultivars in the Shanghai region of China. Genet Mol Res 11:644–650

    CAS  PubMed  Google Scholar 

  • Elakhdar A, Abd EL-Sattar M, Amer K, Rady A, Kumamaru T (2016) Population structure and marker–trait association of salt tolerance in barley (Hordeum vulgare L.). C R Biol 339(11–12):454–461

  • Elakhdar A, Kumamaru T, Qualset CO, Brueggeman RS, Amer K, Capo-chichi L (2018) Assessment of genetic diversity in Egyptian barley (Hordeum vulgare L.) genotypes using SSR and SNP markers. Genet Resour Crop Evol 65:1937–1951

    Google Scholar 

  • Eshghi R, Ojaghi J, Salayeva S (2010) Genetic gain through selection indices in hulless barley. Int J Agric Biol 13(2)

  • Fernandez M, Figueiras A, Benito C (2002) The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin. Theor Appl Genet 104:845–851

    CAS  PubMed  Google Scholar 

  • Garcia del Moral LF, Garcia del Moral MB, Molina-Cano L, Slafer GA (2003) Yield stability and development in two- and six-rowed winter barleys under Mediterranean conditions. Field Crops Res 81:109–119

    Google Scholar 

  • Gougerdchi V, Dezhsetan S, Ebrahimi MA, Sadeghzadeh B, Savari S (2014) Using SSR markers for assessment genetic diversity and detection drought escape candidate genes in barley lines (Hordeumvulgare L.). Plant Breed Seed Sci 70:1–14

    Google Scholar 

  • Gougerdchi V, Dezhsetan S, Ebrahimi MA, Sadeghzadeh B, Savari S (2018) Using SSR markers for assessment genetic diversity and detection drought escape candidate genes in barley lines (Hordeum vulgare L.). Plant Breed Seed Sci 70:3–14

    Google Scholar 

  • Gupta PK, Balyan HS, Kulwal PL, Kumar N, Kumar A, Mir RR, Mohan A, Kumar J (2007) QTL analysis for some quantitative traits in bread wheat. J Zhejiang Univ Sci 8:807–814

    Google Scholar 

  • Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18

    CAS  PubMed  Google Scholar 

  • Gupta PK, Kulwal PL, Mir RR (2013a) QTL mapping: methodology and applications in cereal breeding. In: Gupta PK, Varshney RK (eds) Cereal genomics II. Springer, The Netherlands, pp 275–318

    Google Scholar 

  • Gupta PK, Rustgi S, Mir RR (2013b) Array-based high-throughput DNA markers and genotyping platforms for cereal genetics and genomics. In: Gupta PK, Varshney RK (eds) Cereal genomics II. Springer, The Netherlands, pp 11–55

    Google Scholar 

  • Harlan JR (1995) Barley. In: Smartt J, Simmonds NW (eds) Evolution of crop plants, 2nd edn. Longman, London, pp 140–146

    Google Scholar 

  • Ibrahim A, Harrison MT, Meinke H, Zhou M (2011) Examining the yield potential of barley near-isogenic lines using a genotype by environment by management analysis. Eur J Agron 105:41–51

    Google Scholar 

  • Ivandic V, Hackett CA, Nevo E, Keith R, Thomas WTB, Forster BP (2002) Analysis of simple sequence repeats (SSRs) in wild barley from the fertile crecent: associations with ecology, geography and flowering time. Plant Mol Biol 48:511–527

    CAS  PubMed  Google Scholar 

  • Jaiswal V, Mir RR, Mohan A, Balyan HS, Gupta PK (2012) Association mapping for pre-harvest sprouting tolerance in bread wheat (Triticum aestivum L.). Euphytica 188:89–102

    CAS  Google Scholar 

  • Jaiswal V, Gahlaut V, Meher PK, Mir RR, Jaiswal JP, Rao AR, Balyan HS, Gupta PK (2016) Genome wide single locus single trait, multi-locus and multi-trait association mapping for some important agronomic traits in common wheat (T. aestivum L.). PLoS ONE 11(7):e0159343

  • Jalata Z, Mekbib F, Lakew B (2020) Generation mean analysis of net blotch and scald diseases on barley. World 8(4):142–149

    Google Scholar 

  • Kanbar A, Kondo K (2011) Efficiency of ISSR and RAPD dominant markers in assessing genetic diversity among Japanese and Syrian cultivars of barley (H. vulgare L.). Res J Agric Biol Sci 7:4–10

    CAS  Google Scholar 

  • Kulwal PL, Mir RR, Kumar S, Gupta PK (2010) QTL analysis and molecular breeding for seed dormancy and pre-harvest sprouting tolerance in bread wheat. J Plant Biol 37:59–74

    Google Scholar 

  • Kumar J, Mir RR, Kumar N, Kumar A, Mohan A, Prabhu KV, Balyan HS, Gupta PK (2010) Marker assisted selection for pre-harvest sprouting tolerance and leaf rust resistance in bread wheat. Plant Breed 129:617–621

    CAS  Google Scholar 

  • Kumar S, Kumar M, Mir RR, Kumar R, Kumar S (2021) Advances in molecular markers and their use in genetic improvement of wheat. In: Wani SH, Mohan A, Singh GP (eds) Physiological, molecular, and genetic perspectives of wheat improvement, pp 139–174

  • Le Gouis J (1993) Grain filling and shoot growth of two-row and six-row winter barley varieties. Agronomie 13:545–552

    Google Scholar 

  • Le Gouis J, Delebarre O, Beghin D, Heumez E, Pluchard P (1999) Nitrogen uptake and utilisation efficiency of two-row and six-row winter barley cultivars grown at two N levels. Eur J Agron 10:73–79

    Google Scholar 

  • Li CD, Tarr A, Lance RCM, Harasymow S, Uhlmann J, Westcot S, Young KJ, Grime CR, Cakir M, Broughton S, Apples R (2003) A major QTL controlling seed dormancy and preharvest sprouting/grain α-amylase in two-rowed barley (Hordeumvulgare L.). Aust J Agric Res 54:1303–1313

    CAS  Google Scholar 

  • Matus IA, Hayes PM (2002) Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome 45:1095–1106

    CAS  PubMed  Google Scholar 

  • Meszaros K, Karsai I, Kuti C, Banyai J (2007) Efficiency of different marker systems for genotype fingerprinting and for genetic diversity studies in barley (Hordeumvulgare L.). S Afr J Bot 73:43–48

    CAS  Google Scholar 

  • Mir RR, Varshney RK (2013) Future prospects of molecular markers in plants. In: Henry RJ (ed) Molecular markers in plants. Blackwell Publishing Ltd, Oxford, pp 169–190

    Google Scholar 

  • Mir RR, Choudhary N, Bawa V, Jan S, Singh B, Bhat MA, Paliwal R, Gupta A, Chitikineni A, Thudi M, Varshney RK (2021) Allelic diversity, structural analysis and Genome-wide Association Study (GWAS) for yield and related traits using unexplored common bean (Phaseolus vulgaris L.) germplasm from Western Himalayas. Front Genet 11:1797

  • Mir RR, Hiremath PJ, Riera-Lizarazu O, Varshney RK (2013) Evolving molecular marker technologies in plants: from RFLPs to GBS. In: Lübberstedt T, Varshney RK (eds) Diagnostics in plant breeding. Springer, New York, pp 229–247

    Google Scholar 

  • Mir RR, Kumar J, Balyan HS, Gupta PK (2012a) A study of genetic diversity among Indian bread wheat (Triticum aestivum L.) cultivars released during last 100 years. Genet Resour Crop Evol 59:717–726

    CAS  Google Scholar 

  • Mir RR, Kumar N, Jaiswal V, Girdharwal N, Prasad M, Balyan HS, Gupta PK (2012b) Genetic dissection of grain weight (GW) in bread wheat through QTL interval and association mapping. Mol Breed 29:963–972

    Google Scholar 

  • Mohan A, Kulwal PL, Singh R, Kumar V, Mir RR, Kumar J, Prasad M, Balyan HS, Gupta PK (2009) Genome wide QTL analysis for pre-harvest sprouting tolerance in bread wheat. Euphytica 168:319–329

    CAS  Google Scholar 

  • Monawekh R, Azzam H, Abbas S, Murshed R (2014) Use of SSR marker to assessment the genetic diversity of some Hordeum vulgare genotypes. Int J Chemtech Res 6(5):2952–2961

    CAS  Google Scholar 

  • Naceur AB, Chaabane R, El-Faleh M, Abdelly C, Ramla D, Nada A, Sakr M, Naceur MB (2012) Genetic diversity analysis of North Africa’s barley using SSR markers. J Genet Eng Biotechnol 10:13–21

    Google Scholar 

  • Nakamura S (2018) Grain dormancy genes responsible for preventing pre-harvest sprouting in barley and wheat. Breed Sci 68(3):295–304

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nei M (1979) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–190

    Google Scholar 

  • Pandey M, Wagner C, Friedt W, Ordon F (2004) Genetic diversity of hull-less barley (Hordeumvulgare L.) landraces in the highlands of central Nepal as revealed by SSRs. In: Vollmann J, Grausgruber H, Ruckenbauer P (eds) Genetic variation for plant breeding, pp 45–48

  • Pandey M, Wagner C, Friedt W, Ordon F (2006) Genetic relatedness and population differentiation of Himalayan hulless barley (Hordeumvulgare L.) landraces inferred with SSRs. Theoret Appl Genet 113:715–729

    CAS  Google Scholar 

  • Parsad R, Rathore A, Gupta VK (2003) Statistical Package for Augmented Designs (SPAD). IASRI Library Avenue, New Delhi

  • Patel NA, Meena M (2018) Relative performance of barley (Hordeum vulgare L.) cultivars under saline water condition. Int J Curr Microbiol App Sci 7:1724–1733

    CAS  Google Scholar 

  • Pawan K, Tikle AN, Verma RPS, Rekha M (2017) Diversity assessment of hulled barley (Hordeum vulgare L.) accessions by agro-morphological traits and SSR markers. Res J Biotechnol 12:11

  • Peakall ROD, Smouse PE (2006) GENALex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software v. 6.0.010.http://darwin.cirad.fr/

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamic. Proc Natl Acad Sci USA 81:8014–8019

    CAS  PubMed  PubMed Central  Google Scholar 

  • Shafi S, Tahir M, Khan MA, Bhat MA, Kumar U, Kumar S, Mir RR (2021) Trait phenotyping and genic/random SSR markers characterization for breeding early maturing Wheats from Western-Himalayas. Genetic Resources and Crop Evolution (under revision)

  • Sharma R, Draicchio F, Bull H, Herzig P, Maurer A, Pillen K, Thomas TBT, Flavell AJ (2018) Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding. J Exp Bot 69:3811–3822

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sullivan P, Arendt E, Gallagher E (2013) The increasing use of barley and barley by-products in the production of healthier baked goods. Trends Food Sci Technol 29:124–134

    CAS  Google Scholar 

  • Tahir A, Ilyas MK, Sardar MM, Pouya AK, Rasouli F, Bibi A, Ghafoor A (2020) Selection criteria for yield potential in a large collection of Vigna radiata (L.) accessions. Euphytica 216(9):1–12

  • Tahir M, Shafi S, Khan MA, Sheikh FA, Bhat MA, Sofi PA, Kumar S, Wani MA, Mir RR (2021) Grain micronutrient and molecular characterization of wheat (Triticum aestivum L.) germplasm using genic and random SSR Markers. Crop Pasture Sci. https://doi.org/10.1071/CP21116

  • Targais K, Stobdan T, Mundra S, Ali Z, Yadav A, Korekar G, Singh SB (2012) Chhang—a barley based alcoholic beverage of Ladakh, India

  • Tyagi S, Mir RR, Kaur H, Chhuneja P, Ramesh B, Balyan HS, Gupta PK (2014) Marker-assisted pyramiding of eight QTLs/genes for seven different traits in common wheat (Triticum aestivum L.). Mol Breed 34:167–175

    CAS  Google Scholar 

  • Tyagi S, Sharma S, Ganie SA, Tahir M, Mir RR, Pandey R (2019) Plant microRNAs: biogenesis, gene silencing, web-based analysis tools and their use as molecular markers. 3 Biotech 9(11):413

  • Tyagi S, Kumar A, Gautam T, Pandey R, Rustgi S, Mir RR (2021) Development and use of miRNA-derived SSR markers for the study of genetic diversity, population structure, and characterization of genotypes for breeding heat tolerant wheat varieties. PLoS ONE. https://doi.org/10.1371/journal.pone.0231063

    Article  PubMed  PubMed Central  Google Scholar 

  • Ullrich SE (2011) Barley: production, improvement, and uses (vol 12). Wiley

    Google Scholar 

  • Varshney RK, Mahendar T, Aggarwal RK, Borner A (2007) Genic molecular markers in plants: development and application. In: Varshney RK, Tuberosa R (eds) Genomics-assisted crop improvement: vol. 1: genomics approaches and platforms, pp 13–29

  • Varshney RV, Salem KFM, Baum M, Roder MS, Graner A, Borner A (2008) SSR and SNP diversity in a barley germplasm collection. Plant Genet Resour 6:167–174

    CAS  Google Scholar 

  • Vasanthan T, Hoover R (2009) Chapter 16—barley starch: production, properties, modification and uses. James BM, Roy W (eds) In food science and technology, starch, 3rd ed. Academic Press, pp 601–628

  • Wang J, Yang J, Zhu J, Jia Q, Tao Y (2010) Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding. J Zhejiang Univ Sci B 11:792–800

    PubMed  PubMed Central  Google Scholar 

  • Xu Q, Zeng X, Lin B, Li Z, Yuan H, Wang, Y, Tashi N (2017) A microsatellite diversity analysis and the development of core-set germplasm in a large hulless barley (Hordeum vulgare L.) collection. BMC Genetics 18:102

  • Xhulaji D, Hobdari V, Elezi F 2018. Evaluation of morphological diversity pattern in the Albanian barley (Hordeum vulgare L.) base collection. Albanian J Agric Sci 22–29

  • Yadav SK, Singh AK, Malik R (2015) Genetic diversity analysis based on morphological traits and microsatellite markers in barley (Hordeumvulgare). Indian J Agric Sci 85:37–44

    Google Scholar 

  • Yang JL, Yen CB, Lu R, Bothmer VR (1987) The genus Hordeum (Gramineae) in China variation and distribution. Willdenowia 16:479–490

    Google Scholar 

  • Zhang D, Ding Y (2007) Genetic diversity of wild close relatives of barley in Tibet of China revealed by AFLP. Yi Chuan 29:725–730

    PubMed  Google Scholar 

  • Zhang DL, Gao HY, Li SP (2007) Analysis of genetic diversity on beer barley varieties in China by SSR. Acta Agric Bor Sin 16:72–76

    CAS  Google Scholar 

Download references

Acknowledgements

The authors are thankful to Indian Institute of Wheat and Barley Research (IIWBR), Karnal, Haryana and National Bureau of Plant Genetic Resources (NBPGR), New Delhi, India for sharing their material to carry out this research. The authors are highly thankful to Dean, Faculty of Agriculture, SKUAST-K and Head Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-K for providing facilities to carry out this study.

Author information

Authors and Affiliations

  1. Division of Genetics and Plant Breeding, Faculty of Agriculture (FOA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore, Jammu and Kashmir, 193201, India

    Sami Jan, M. N. Khan, Sofora Jan, Aaqif Zaffar, M. A. Khan, F. A. Sheikh, M. Ashraf Bhat & R. R. Mir

  2. Highland Agricultural Research & Extension Station, SKUAST-K, Zanskar, Jammu and Kashmir, India

    Rizwan Rashid

Authors
  1. Sami Jan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. N. Khan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sofora Jan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Aaqif Zaffar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rizwan Rashid
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M. A. Khan
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. F. A. Sheikh
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. M. Ashraf Bhat
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. R. R. Mir
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. R. Mir.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 16 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jan, S., Khan, M.N., Jan, S. et al. Trait phenotyping and molecular marker characterization of barley (Hordeum vulgare L.) germplasm from Western Himalayas. Genet Resour Crop Evol 69, 661–676 (2022). https://doi.org/10.1007/s10722-021-01251-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-021-01251-z

Keywords

Search

Navigation