Complex patterns of autopolyploid evolution in alfalfa and allies (<i>Medicago sativa</i>; Leguminosae)

Havananda, Tee; Brummer, E. Charles; Doyle, Jeff J.

doi:10.3732/ajb.1000318

Cited by 35 publications

(39 citation statements)

References 75 publications

(103 reference statements)

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“…Although the data are generally consistent with recurrent polyploidization and interploidy gene flow, nuclear gene sequences also support the existence of a bottleneck in the domestication of at least some alfalfa populations [15]. Tetraploid falcata origins appear to be more complex, with some evidence of introgression from M. prostrata [13]. Mixing between cultivated and wild populations has been documented [16], but some wild populations appear to have remained distinct despite cultivars being grown in the vicinity [17].…”

Section: Alfalfa Origins and Genetic Diversitymentioning

confidence: 50%

“…Examination of mitochondrial, chloroplast, and nuclear genes and DNA markers clearly show that sativa is the tetraploid form of caerulea [13][14][15]. Although the data are generally consistent with recurrent polyploidization and interploidy gene flow, nuclear gene sequences also support the existence of a bottleneck in the domestication of at least some alfalfa populations [15].…”

Section: Alfalfa Origins and Genetic Diversitymentioning

confidence: 61%

“…An extensive examination of wild diploid germplasm using simple sequence repeat (SSR) markers showed that falcata and caerulea accessions are clearly distinct, with hybrids falling in between the separate parental groups [10,11]. Falcata and sativa are similarly distinct, based on numerous experiments conducted on tetraploid populations [9,12,13].…”

Section: Alfalfa Origins and Genetic Diversitymentioning

confidence: 99%

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Applied Genetics and Genomics in Alfalfa Breeding

2012

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Alfalfa (Medicago sativa L.), a perennial and outcrossing species, is a widely planted forage legume for hay, pasture and silage throughout the world. Currently, alfalfa breeding relies on recurrent phenotypic selection, but alternatives incorporating molecular marker assisted breeding could enhance genetic gain per unit time and per unit cost, and accelerate alfalfa improvement. Many major quantitative trait loci (QTL) related to agronomic traits have been identified by family-based QTL mapping, but in relatively large genomic regions. Candidate genes elucidated from model species have helped to identify some potential causal loci in alfalfa mapping and breeding population for specific traits. Recently, high throughput sequencing technologies, coupled with advanced bioinformatics tools, have been used to identify large numbers of single nucleotide polymorphisms (SNP) in alfalfa, which are being developed into markers. These markers will facilitate fine mapping of quantitative traits and genome wide association mapping of agronomic traits and further advanced breeding strategies for alfalfa, such as marker-assisted selection and genomic selection. Based on ideas from the literature, we suggest several ways to improve selection in alfalfa including (1) diversity selection and paternity testing, (2) introgression of QTL and (3) genomic selection.

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Section: Alfalfa Origins and Genetic Diversitymentioning

confidence: 50%

Section: Alfalfa Origins and Genetic Diversitymentioning

confidence: 61%

Section: Alfalfa Origins and Genetic Diversitymentioning

confidence: 99%

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Applied Genetics and Genomics in Alfalfa Breeding

2012

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“…The Medicago sativa-falcata complex is an attractive model system for studying infraspecific hybridization between alien domesticated taxa and their wild congeners (Quiros and Bauchan 1988;Muller et al 2003;Havananda et al 2011;Lapiņ a et al 2011;Kaljund and Leht 2013). This polymorphic species complex consists of several taxa that are diploid and/or tetraploid, including M. sativa subsp.…”

Section: Introductionmentioning

confidence: 99%

ISSR and chloroplast DNA analyses indicate frequent hybridization of alien Medicago sativa subsp. sativa and native M. sativa subsp. falcata

et al. 2015

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ISSR and chloroplast DNA analyses indicate frequent hybridization of alien Medicago sativa subsp. sativa and native M. sativa subsp. falcata Abstract Alfalfa (Medicago sativa subsp. sativa) was introduced to Lithuania as a fodder crop and now grows as a weed in natural ecosystems adjacent to its wild relative, sickle medic (M. sativa subsp. falcata). The hybrid form of these taxa, variegated alfalfa (M. sativa subsp. varia), is considered an invasive taxon due to its intensive spread. Here, we use inter-simple sequence repeat (ISSR) markers and haplotype analyses of three regions of chloroplast DNA (psbA-trnH, trnS-trn2GS and trnL-trnF) and the nuclear ribosomal DNA internal transcribed spacer region to study the spontaneous hybridization of alfalfa and sickle medic in natural subpopulations. Plants of the three taxa were collected from 19 subpopulations located at seven sites. ISSR analysis revealed similar values of genetic diversity (expected heterozygosity, band richness, polymorphic band proportion) in subpopulations of the three studied subspecies. Our study revealed a lack of genetic differentiation among these taxa and high differentiation among subpopulations (U ST = 0.389, P = 0.001). Analysis of the chloroplast DNA regions provides direct evidence for the hybrid origin of variegated alfalfa. Taxon-characteristic haplotypes were identified for subsp. sativa and subsp. falcata in local subpopulations, and two haplotypes specific to the parental taxa were detected in subpopulations of M. sativa subsp. varia. Our study demonstrates the extensive genetic impact of alfalfa on adjacent native subpopulations of sickle medic.

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“…Autopolyploidy is a common occurrence in the evolutionary history of many plant species (Cui et al, 2006;Havananda et al, 2011;Parisod et al, 2016). Like many angiosperms, Brassica rapa underwent several rounds of whole genome duplication during its evolutionary history (Tang & Lyons, 2012).…”

Section: Introductionmentioning

confidence: 99%

Genes Encoding Flower- and Root-Specific Functions are More Resistant to Fractionation than Globally Expressed Genes in Brassica rapa

Kolkailah¹

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Like many angiosperms, Brassica rapa underwent several rounds of whole genome duplication during its evolutionary history. Brassica rapa is particularly valuable for studying genome evolution because it also experienced whole genome triplication shortly after it diverged from the common ancestor it shares with Arabidopsis thaliana about 17-20 million years ago. While many B. rapa genes appear resistant to paralog retention, close to 50% of B. rapa genes have retained multiple, paralogous loci for millions of years and appear to be multi-copy tolerant. Based on previous studies, gene function may contribute to the selective pressure driving certain genes back to singleton status. It is suspected that other factors, such as gene expression patterns, also play a role in determining the fate of genes following whole genome triplication. Published RNA-seq data was used to determine if gene expression patterns influence the retention of extra gene copies. It is hypothesized that retention of genes in duplicate and triplicate is more likely if those genes are expressed in a tissue-specific manner, as opposed to being expressed globally across all tissues. This study shows that genes expressed specifically in flowers and roots in B. rapa are more resistant to fractionation than globally expressed genes following whole genome triplication. In particular, there appears to have been selection on genes expressed specifically in flower tissues to retain higher copy numbers and for all three copies to exhibit the same flower-specific expression pattern. Future research to determine if these observations in Brassica rapa are consistent with other angiosperms that have undergone recent whole genome duplication would confirm that retention of flower-specific-expressed genes is a general feature in plant genome evolution and not specific to B. rapa.

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Complex patterns of autopolyploid evolution in alfalfa and allies (Medicago sativa; Leguminosae)

Cited by 35 publications

References 75 publications

Applied Genetics and Genomics in Alfalfa Breeding

Applied Genetics and Genomics in Alfalfa Breeding

ISSR and chloroplast DNA analyses indicate frequent hybridization of alien Medicago sativa subsp. sativa and native M. sativa subsp. falcata

Genes Encoding Flower- and Root-Specific Functions are More Resistant to Fractionation than Globally Expressed Genes in Brassica rapa

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