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An Irish perennial ryegrass genetic resource collection clearly divides into two major gene pools

Published online by Cambridge University Press:  07 December 2015

Susanne Barth ,
Sarah Katherine McGrath ,
Sai Krishna Arojju  and
Trevor Roland Hodkinson
Susanne Barth*
Affiliation:
Teagasc Crops Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland
Sarah Katherine McGrath
Affiliation:
Teagasc Crops Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland Department of Botany, School of Natural Sciences, Trinity College Dublin, Ireland
Sai Krishna Arojju
Affiliation:
Teagasc Crops Environment and Land Use Programme, Oak Park Research Centre, Carlow, Ireland Department of Botany, School of Natural Sciences, Trinity College Dublin, Ireland
Trevor Roland Hodkinson
Affiliation:
Department of Botany, School of Natural Sciences, Trinity College Dublin, Ireland
*
*Corresponding author. E-mail: [email protected]
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Abstract

This study assessed the genetic diversity in 928 individuals from 40 diploid populations of Lolium perenne using nuclear simple sequence repeat markers, including 22 accessions of Irish ecotypes, seven European ecotypes and 11 released varieties. High levels of allelic and genetic diversity were determined, with intra-population variation accounting for the majority of the variation. The majority of the accessions deviated from Hardy–Weinberg equilibrium and had relatively high inbreeding coefficients. Two major gene pools of ecotypic accessions were defined by unweighted pair group method with arithmetic mean (UPGMA) and PCA analyses. One of these two gene pools accounted for two-thirds of the ecotypes and included most of the current Irish and Northern Irish breeding materials and about half of the European ecotypes included in this study; these European ecotypes performed well under Irish selection conditions. Population structure and differentiation analyses using Structure analysis and analysis of molecular variance confirmed the results found in the UPGMA and PCA analyses. These results will be useful for breeders who wish to exploit specific pools from ecotype collections.

Keywords

genetic diversitygenetic resourcesLolium perenneperennial ryegrasspopulation structureSSR markers
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 3 , June 2017 , pp. 269 - 278
Copyright
Copyright © NIAB 2015 

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References

Auzanneau, J, Huyghe, C, Julier, B and Barre, P (2007) Linkage disequilibrium in synthetic varieties of perennial ryegrass. Theoretical and Applied Genetics 115: 837–847.Google Scholar
Berg, EE and Hamrick, JL (1995) Fine-scale genetic structure of a Turkey oak forest. Evolution 49: 110–120.CrossRefGoogle ScholarPubMed
Blackmore, T, Thomas, I, McMahon, R, Powell, W and Hegarty, M (2015) Genetic–geographic correlation revealed across a broad European ecotypic sample of perennial ryegrass (Lolium perenne) using array-based SNP genotyping. Theoretical and Applied Genetics 128: 1917–1932.Google Scholar
Bolaric, S, Barth, S, Melchinger, AE and Posselt, UK (2005a) Genetic diversity in European perennial ryegrass cultivars investigated with RAPD markers. Plant Breeding 124: 161–166.Google Scholar
Bolaric, S, Barth, S, Melchinger, AE and Posselt, UK (2005b) Molecular genetic diversity within and among German ecotypes in comparison to European perennial ryegrass cultivars. Plant Breeding 124: 257–262.CrossRefGoogle Scholar
Botstein, D, White, R, Skolnick, M and Davis, R (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 3: 314–331.Google Scholar
Central Statistics Office (2012) Census of Agriculture 2010 – Final Results. Dublin: The Stationery Office.Google Scholar
Charlesworth, D and Wright, SI (2001) Breeding systems and genome evolution. Current Opinion in Genetics and Development 11: 685–690.Google Scholar
Cresswell, A, Hamilton, NRS, Roy, AK and Viegas, BMF (2001) Use of amplified fragment length polymorphism markers to assess genetic diversity of Lolium species from Portugal. Molecular Ecology 10: 229–241.CrossRefGoogle ScholarPubMed
Earl, D and vonHoldt, B (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359–361.CrossRefGoogle Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Excoffier, L, Smouse, PE and Quattro, JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479–491.Google Scholar
Falush, D, Stephens, M and Pritchard, JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.CrossRefGoogle ScholarPubMed
Falush, D, Stephens, M and Pritchard, JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology 7: 574–578.Google Scholar
Gill, GP, Wilcox, PL, Whittaker, DJ, Winz, RA, Bickerstaff, P, Echt, CE, Kent, J, Humphreys, MO, Elborough, KM and Gardner, RC (2006) A framework linkage map of perennial ryegrass based on SSR markers. Genome 49: 354–364.Google Scholar
Guo, S and Thompson, E (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48: 361–371.Google Scholar
Guthridge, KM, Dupal, MP, Kolliker, R, Jones, ES, Smith, KF and Forster, JW (2001) AFLP analysis of genetic diversity within and between populations of perennial ryegrass (Lolium perenne L.). Euphytica 122: 191–201.Google Scholar
Jakobsson, M and Rosenberg, NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801–1806.Google Scholar
Jones, ES, Dupal, MP, Kolliker, R, Drayton, MC and Forster, JW (2001) Development and characterisation of simple sequence repeat (SSR) markers for perennial ryegrass. Theoretical and Applied Genetics 102: 405–415.CrossRefGoogle Scholar
Kolliker, R, Stadelmann, FJ, Reidy, B and Nosberger, J (1999) Genetic variability of forage grass cultivars: a comparison of Festuca pratensis Huds., Lolium perenne L., and Dactylis glomerata L. Euphytica 106: 261–270.CrossRefGoogle Scholar
Kubik, C, Sawkins, M, Meyer, WA and Gaut, BS (2001) Genetic diversity in seven perennial ryegrass (Lolium perenne L.) cultivars based on SSR markers. Crop Science 41: 1565–1572.CrossRefGoogle Scholar
Lem, P and Lallemand, J (2003) Grass consensus STS markers: an efficient approach for detecting polymorphism in Lolium . Theoretical and Applied Genetics 107: 1113–1122.Google Scholar
McGrath, S, Hodkinson, TR and Barth, S (2007) Extremely high cytoplasmic diversity in natural and breeding populations of Lolium (Poaceae). Heredity (Edinburgh) 99: 531–544.CrossRefGoogle ScholarPubMed
McGrath, S, Hodkinson, TR, Charles, TM, Zen, DG and Barth, S (2010) Variation in inflorescence characters and inflorescence development in ecotypes and cultivars of Lolium perenne L. Grass and Forage Science 65: 398–409.Google Scholar
McGrath, S, Hodkinson, TR, Frohlich, A, Grant, J and Barth, S (2014) Seasonal and genetic variations in water-soluble carbohydrates and other quality traits in ecotypes and cultivars of perennial ryegrass (Lolium perenne L.). Plant Genetic Resources 12: 236–247.CrossRefGoogle Scholar
Momotaz, A, Forster, JW and Yamada, T (2004) Identification of cultivars and accessions of Lolium, Festuca and Festulolium hybrids through the detection of simple sequence repeat polymorphism. Plant Breeding 123: 370–376.CrossRefGoogle Scholar
Nei, M (1972) Genetic distance between populations. The American Naturalist 106: 283–292.CrossRefGoogle Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America 70: 3321–3323.Google Scholar
Ponting, RC, Drayton, MC, Cogan, NOI, Dobrowolski, MP, Spangenberg, GC, Smith, KF and Forster, JW (2007) SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.). Molecular Genetics and Genomics 278: 585–597.Google Scholar
Pritchard, JK, Stephens, M, Rosenberg, NA and Donnelly, P (2000 a) Association mapping in structured populations. American Journal of Human Genetics 67: 170–181.Google Scholar
Pritchard, JK, Stephens, M and Donnelly, P (2000 b) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Ramasamy, RK, Ramasamy, S, Bindroo, BB and Naik, VG (2014) STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface. SpringerPlus 3: 431.Google Scholar
Rohlf, F (2005) NTSYSpc: Numerical Taxonomy System. Setauket, NY: Exeter Publishing Ltd.Google Scholar
Roldan-Ruiz, I, Calsyn, E, Gilliland, TJ, Coll, R, van Eijk, MJT and De Loose, M (2000) Estimating genetic conformity between related ryegrass (Lolium) varieties. 2. AFLP characterization. Molecular Breeding 6: 593–602.Google Scholar
Roldan-Ruiz, I, van Eeuwijk, FA, Gilliland, TJ, Dubreuil, P, Dillmann, C, Lallemand, J, De Loose, M and Baril, CP (2001) A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties. Theoretical and Applied Genetics 103: 1138–1150.CrossRefGoogle Scholar
Rosenberg, NA, Pritchard, JK, Weber, J, Cann, HM, Kidd, KK, Zhivotovsky, LA and Feldman, MW (2002) Genetic structure of human populations. Science 298: 2381–2385.Google Scholar
Salamin, N, Hodkinson, TR and Savolainen, V (2005) Towards building the tree of life: a simulation study for all angiosperm genera. Systematic Biology 54: 183–196.CrossRefGoogle ScholarPubMed
Schneider, S, Roessli, D and Excoffier, L (2000) Arlequin Ver. 2.000: A Software for Population Genetics Data Analysis. Geneva, Switzerland: Genetics and Biometry Laboratory, University of Geneva.Google Scholar
Skøt, L, Hamilton, NRS, Mizen, S, Chorlton, KH and Thomas, ID (2002) Molecular genecology of temperature response in Lolium perenne: 2. Association of AFLP markers with ecogeography. Molecular Ecology 11: 1865–1876.CrossRefGoogle ScholarPubMed
Skøt, L, Humphreys, MO, Armstead, I, Heywood, S, Skøt, KP, Sanderson, R, Thomas, ID, Chorlton, KH and Hamilton, NRS (2005) An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Molecular Breeding 15: 233–245.Google Scholar
Sneath, P and Sokal, R (1973) Numerical Taxonomy. San Francisco: W.H. Freeman and Company.Google Scholar
Studer, B, Widmer, F, Enkerli, J and Kolliker, R (2006) Development of novel microsatellite markers for the grassland species Lolium multiflorum, Lolium perenne and Festuca pratensis . Molecular Ecology Notes 6: 1108–1110.CrossRefGoogle Scholar
Turner, LB, Cairns, AJ, Armstead, IP, Ashton, J, Skøt, K, Whittaker, D and Humphreys, MO (2006) Dissecting the regulation of fructan metabolism in perennial ryegrass (Lolium perenne) with quantitative trait locus mapping. New Phytologist 169: 45–57.Google Scholar
Van Treuren, R, Bas, N, Goossens, PJ, Jansen, J and Van Soest, JM (2005) Genetic diversity in perennial ryegrass and white clover among old Dutch grasslands as compared to cultivars and nature reserves. Molecular Ecology 14: 39–52.Google Scholar
Warnke, SE, Barker, RE, Jung, G, Sim, SC, Rouf Mian, MA, Saha, MC, Brilman, LA, Dupal, MP and Forster, JW (2004) Genetic linkage mapping of an annual × perennial ryegrass population. Theoretical and Applied Genetics 109: 294–304.Google Scholar
Weir, BS and Cockerham, CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.Google Scholar
Xing, Y, Frei, U, Schejbel, B, Asp, T and Lubberstedt, T (2007) Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne . BMC Plant Biology 7: 43.Google Scholar
Yeh, FC and Boyle, T (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian Journal of Botany 129: 157–163.Google Scholar
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