Gene-Based Sequence Diversity Analysis of Field Pea (Pisum)

Abstract

Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the species. The data set yields a genetic diversity tree whose deep branches, involving wild samples, are preserved in a tree derived from a polymorphic retrotransposon insertions in an identical sample set. Thus, gene regions and intergenic ''junk DNA'' share a consistent picture for the genomic diversity of Pisum, despite low linkage disequilibrium in wild and landrace germplasm, which might be expected to allow independent evolution of these very different DNA classes. Additional lines of evidence indicate that recombination has shuffled gene haplotypes efficiently within Pisum, despite its high level of inbreeding and widespread geographic distribution. Trees derived from individual gene loci show marked differences from each other, and genetic distance values between sample pairs show high standard deviations. Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, phylogenetic network analysis confirms the non-treelike structure of Pisum diversity and indicates the major germplasm classes involved. Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species.T HE genetic diversity of a species is the sum of its total DNA sequence variation, resulting from millions of years of cumulative mutation, recombination, and selection. Understanding the pattern of the diversity within cultivated plant species and their wild relatives is both interesting and practically important from the viewpoint of conservation and use. Therefore, the ways by which genetic diversity in populations are estimated and represented are important. A popular approach for measuring the genetic diversity of accessions of a species is to analyze samples from gene banks (germplasm collections) by one or more of the many available molecular marker methods. The effectiveness of this strategy depends upon the suitability of the marker method for analyzing the diversity of the sample collection under investigation. Different marker methods can give different views of diversity, depending upon the evolutionary parameters of the underlying DNA sequence variation. Rapidly evolving DNAs, such as simple sequence repeats (SSRs), give high resolution views of relatedness; single nucleotide polymorphism (SNP)-based variation is more suited to deeper relationships, reflecting the slow mutation rate for this type of sequence variation; and transposon insertion-based marker methods should lie between these two, reflecting their intermediate mutation rate, although few studies have been carried out to test this. Furthermore, the g...

Legume Crops Phylogeny and Genetic Diversity for Science and Breeding

“…The most appropriate status for P. sativum subsp. abyssinicum is still under debate, as it has been resurrected as a third species by some authors (Maxted and Ambrose, 2001;Vershinin et al, 2003;Jing et al, 2007). The most recent studies place it between P. fulvum Sibth.…”

“…Different molecular techniques were applied over the last two decades to study pea genetic diversity. Using these markers, several major world pea germplasm collections have been analyzed and representative core collections formed (Baranger et al, 2004;Loridon et al, 2005;Jing et al, 2005Jing et al, , 2007Jing et al, , 2010Jing et al, , 2012Smýkal et al, 2008aSmýkal et al, , 2011Smýkal et al, , 2013Zong et al, 2009;Nasiri et al, 2010;Kwon et al, 2012;Majeed et al, 2012). All these studies give a consistent view: the Pisum genus is very diverse, and the diversity is structured, showing a range of degrees of relatedness that reflect taxonomic identifiers, eco-geography and breeding gene pools (Ellis, 2011;Jing et al, 2012;Smýkal et al, 2011Smýkal et al, , 2013.…”

“…With advances in model legume sequencing and genomic knowledge, there has been a switch to gene-based markers in pea (Aubert et al, 2006;Jing et al, 2007;Deulvot et al, 2010;Bordat et al, 2011). Recently, a comprehensive transcriptome of pea was published (Franssen et al, 2011), and another RNA-seq atlas is being established at INRA, France (http://bios.dijon.inra.fr).…”

B chromosome in Plantago lagopus Linnaeus, 1753 shows preferential transmission and accumulation through unusual processes

“…SSAP has also been used for the recombination studies in the selfed progeny plants of Pisum Linnaeus, 1753 (Jing et al 2007). The marker has been used to detect the variation at genic level due to recombination and the combination of male and female genome mutation.…”

Genome diversity in wild grasses under environmental stress

“…It is clear that genetic variation can result from natural selection of genotypes that are adapted to particular environments. Furthermore, different loci within any one genome may experience different selection pressures, which can result in widely varying allelic diversity among genes within the same plant species (2). Several recent studies have assessed the relationship of environmental conditions to genetic diversity in wild plant populations (3)(4)(5)(6)(7).…”