Domestication history in the Medicago sativa species complex: inferences from nuclear sequence polymorphism

Abstract

DNA sequence polymorphism carries genealogical information and allows for testing hypotheses on selection and population history, especially through coalescent-based analysis. Understanding the evolutionary forces at work in plant domestication and subsequent selection is of critical importance for the management of genetic resources. In this study, we surveyed DNA sequence diversity at two assumed neutral nuclear loci in the wild-domesticated species complex of alfalfa (Medicago sativa L.). A high level of polymorphism was detected. The domesticated pool contains on average 31% less diversity than the wild pool, but with a high heterogeneity among loci. Coalescent simulations of the domestication process showed that this result cannot be explained by assuming a constant population size but is rather consistent with a demographic bottleneck during domestication. A very low level of divergence was detected between the wild and the domesticated forms as well as between the related subspecies of the M. sativa species complex. However, the originality of the Spanish wild populations, already observed based on mitochondrial DNA polymorphism, was confirmed. These results, together with patterns of intrapopulation polymorphism, suggest that nuclear sequence polymorphism could be a promising tool, complementary to mitochondrial DNA and phenotypic evaluations, to investigate historical demographic and evolutionary processes.

Applied Genetics and Genomics in Alfalfa Breeding

“…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]. Tetraploid falcata origins appear to be more complex, with some evidence of introgression from M. prostrata [13].…”

Achievements and Challenges in Improving Temperate Perennial Forage Legumes

“…Polyploidy generates increased size of vegetative and reproductive organs, justifying the selection of polyploidy forms for cultivation. Molecular data suggest that cultivated alfalfa lost about 30% of its genetic diversity compared to wild populations during domestication (Muller et al, 2006), although transcript profiling of a limited number of wild diploid and cultivated tetraploid genotypes suggested allelic loss closer to 9% .…”

“…Studies of molecular diversity are increasingly performed on genetic resources of red clover, alfalfa and white clover with different objectives, such as exploring phylogenetical or evolutive relationships (e.g., Muller et al, 2006), investigating the genetic structure of populations (e.g., Crochemore et al, 1996), assessing innovative procedures for variety distinctness (e.g., George et al, 2006), identifying genetically-contrasting material for inclusion in semi-hybrids or in narrowly-based synthetic varieties (e.g., Scotti et al, 2011), and predicting the patterns of variation between populations that could be expected for morphophysiological traits. The latter aim has great practical importance for establishing core collections or choosing subsets of populations for evaluation activities, but requires fairly good consistency between molecular and morphophysiological information.…”

Relationships among Diploid Members of the Medicago sativa (Fabaceae) Species Complex Based on Chloroplast and Mitochondrial DNA Sequences

“…Within the complex, genetic variation within and among subspecies and populations was evaluated previously using several molecular markers: Brummer et al (1991) and Kidwell et al (1994) with nuclear restriction fragment length polymorphism (RFLP); Diwan et al (1997) and Falahati-Anbaran et al (2007) with simple sequence repeats (SSR); Ghérardi et al (1998) with randomly amplified polymorphic DNA (RAPD); Segovia-Lerma et al (2003) with amplified fragment length polymorphism (AFLP); Skinner (2000) with fragment length polymorphism in cpDNA hypervariable regions; Muller et al (2001Muller et al ( , 2003 with mtDNA RFLP; and Muller et al (2006) with nDNA sequences. These studies gave similar results showing considerable genetic variation within and among the accessions included in each study, the majority of which were cultivated accessions of "falcata" and subsp.…”