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      Germplasm dynamics: the role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne

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          Abstract

          Perennial ryegrass ( Lolium perenne) is the most widely grown temperate grass species globally. Intensive plant breeding in ryegrass compared to many other crops species is a relatively recent exercise (last 100 years) and provides an interesting experimental system to trace the extent, impact and trajectory of undomesticated ecotypic variation represented in modern ryegrass cultivars. To explore germplasm dynamics in Lolium perenne, 2199 SNPs were genotyped in 716 ecotypes sampled from 90 European locations together with 249 cultivars representing 33 forage/amenity accessions. In addition three pseudo-cross mapping populations (450 individual recombinants) were genotyped to create a consensus genetic linkage map. Multivariate analyses revealed strong differentiation between cultivars with a small proportion of the ecotypic variation captured in improved cultivars. Ryegrass cultivars generated as part of a recurrent selection programme (RSP) are strongly associated with a small number of geographically localised Italian ecotypes which were among the founders of the RSP. Changes in haplotype frequency revealed signatures of selection in genes putatively involved in water-soluble carbohydrate (WSC) accumulation (a trait selected in the RSP). Retrospective analysis of germplasm in breeding programmes (germplasm dynamics) provides an experimental framework for the identification of candidate genes for novel traits such as WSC accumulation in ryegrass.

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          Evolution of crop species: genetics of domestication and diversification.

          Rachel S Meyer, Michael Purugganan (2013)
          Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.
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            Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare.

            Katherine Caldwell, Joanne Russell, Peter Langridge … (2006)
            In human genetics a detailed knowledge of linkage disequilibrium (LD) is considered a prerequisite for effective population-based, high-resolution gene mapping and cloning. Similar opportunities exist for plants; however, differences in breeding system and population history need to be considered. Here we report a detailed study of localized LD in different populations of an inbreeding crop species. We measured LD between and within four gene loci within the region surrounding the hardness locus in three different gene pools of barley (Hordeum vulgare). We demonstrate that LD extends to at least 212 kb in elite barley cultivars but is rapidly eroded in related inbreeding ancestral populations. Our results indicate that haplotype-based sequence analysis in multiple populations will provide new opportunities to adjust the resolution of association studies in inbreeding crop species.
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              Genomics of gene banks: A case study in rice.

              Susan R McCouch, Kenneth L McNally, Wen Wang … (2012)
              Only a small fraction of the naturally occurring genetic diversity available in the world's germplasm repositories has been explored to date, but this is expected to change with the advent of affordable, high-throughput genotyping and sequencing technology. It is now possible to examine genome-wide patterns of natural variation and link sequence polymorphisms with downstream phenotypic consequences. In this paper, we discuss how dramatic changes in the cost and efficiency of sequencing and genotyping are revolutionizing the way gene bank scientists approach the responsibilities of their job. Sequencing technology provides a set of tools that can be used to enhance the quality, efficiency, and cost-effectiveness of gene bank operations, the depth of scientific knowledge of gene bank holdings, and the level of public interest in natural variation. As a result, gene banks have the chance to take on new life. Previously seen as "warehouses" where seeds were diligently maintained, but evolutionarily frozen in time, gene banks could transform into vibrant research centers that actively investigate the genetic potential of their holdings. In this paper, we will discuss how genotyping and sequencing can be integrated into the activities of a modern gene bank to revolutionize the way scientists document the genetic identity of their accessions; track seed lots, varieties, and alleles; identify duplicates; and rationalize active collections, and how the availability of genomics data are likely to motivate innovative collaborations with the larger research and breeding communities to engage in systematic and rigorous phenotyping and multilocation evaluation of the genetic resources in gene banks around the world. The objective is to understand and eventually predict how variation at the DNA level helps determine the phenotypic potential of an individual or population. Leadership and vision are needed to coordinate the characterization of collections and to integrate genotypic and phenotypic information in ways that will illuminate the value of these resources. Genotyping of collections represents a powerful starting point that will enable gene banks to become more effective as stewards of crop biodiversity.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Sci Rep
                Journal ID (iso-abbrev): Sci Rep
                Title: Scientific Reports
                Publisher: Nature Publishing Group
                ISSN (Electronic): 2045-2322
                Publication date (Electronic): 03 March 2016
                Publication date Collection: 2016
                Volume: 6
                Electronic Location Identifier: 22603
                Affiliations
                [1 ]Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth , Ceredigion, Wales. SY23 3EE.
                Author notes
                Article
                Publisher Item ID: srep22603
                DOI: 10.1038/srep22603
                PMC ID: 4776279
                PubMed ID: 26935901
                SO-VID: 4021ea4d-d03e-4715-9029-ba5b3050ebf8
                Copyright © Copyright © 2016, Macmillan Publishers Limited
                License:

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                Date received : 20 October 2015
                Date accepted : 05 February 2016
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                Subject: Article

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