A novel statistical method for assessing SSR variation in autotetraploid alfalfa (Medicago sativa L.)

Abstract

The level of variation of simple sequence repeat (SSR) markers in cultivated alfalfa from American, Australian and Chinese sources was evaluated using a novel autotetraploid statistical method to calculate the effective number of alleles, the allele frequencies and heterozygosity. We used 19 SSR primers to screen seven polymorphic SSR loci in 320 plants from eight populations. The genetic distance and phylogenetic analysis (DISPAN) program was used to calculate the inter-and intra-population genetic relationships using the conventional binary absence/presence (0/1) method and our novel autotetraploid method. The autotetraploid method resulted in significantly higher heterozygosity (p < 0.01), average effective number (p < 0.01) and lower standard genetic distance (p < 0.01) than the binary method. Our results suggest that our new autotetraploid method is a very useful tool for assessing genetic variation and genetic relationships in all autotetraploid plant species.

The development of 204 novel EST-SSRs and their use for genetic diversity analyses in cultivated alfalfa

“…1). This result showed a high level of polymorphism in alfalfa, as suggested previously (Liu et al, 2007;Wang et al, 2013Wang et al, , 2014. The estimates of polymorphisms are comparable to those reported for 27 EST-SSRs with the same statistical method in alfalfa (mean alleles per locus, Ho, He and H'c of 6.11, 0.64, 0.64 and 1.23, respectively;Liu et al, 2013).…”

“…The observed heterozygosity (Ho) was calculated as previously shown (Liu et al, 2007), and the corrected heterozygosity (He, corrected for sample size) and ShannoneWiener diversity index (H'c, corrected for sample size) were analysed using the ATETRA 1.2.a software program. Only specific bands that could be unambiguously scored across all individual plants were used in this study.…”

Global Transcriptome Sequencing Using the Illumina Platform and the Development of EST-SSR Markers in Autotetraploid Alfalfa

“…This result indicated a high level of polymorphism in alfalfa, as suggested previously [34,49]. This result may be due to a very high cross-pollination and autotetraploidy in this species.…”

Polyploid origin, genetic diversity and population structure in the tetraploid sea lavender Limonium narbonense Miller (Plumbaginaceae) from eastern Spain

“…Similarly, the levels of genetic diversity, which depend not only on the presence/absence of alleles but also on their frequencies can, to some extent, be imperfectly estimated. Nonetheless, several studies based on allozymes have inferred tetraploid genotypes based on the intensity of bands in the zymograms (López-Pujol et al 2004 and novel analytical frameworks for microsatellite markers have been developed allowing the estimation of the number of allele copies and, consequently, individual genotypes in polyploid species Luo et al 2006;Obbard et al 2006;Liu et al 2007). Some analytical methods have also implemented the modification of population genetic statistics to accommodate genomic attributes of polyploids and their different genetic behaviours (i.e.…”