Abstract
To assess the genetic diversity and population structure of Lolium species, we used 32 nuclear simple sequence repeat (SSR) markers and 7 cytoplasmic gene markers to analyze a total of 357 individuals from 162 accessions of 9 Lolium species. This survey revealed a high level of polymorphism, with an average number of alleles per locus of 23.59 and 5.29 and an average PIC-value of 0.83 and 0.54 for nuclear SSR markers and cytoplasmic gene markers, respectively. Analysis of molecular variance (AMOVA) revealed that 16.27 and 16.53% of the total variation was due to differences among species, with the remaining 56.35 and 83.47% due to differences within species and 27.39 and 0% due to differences within individuals in 32 nuclear SSR markers set and 6 chloroplast gene markers set, respectively. The 32 nuclear SSR markers detected three subpopulations among 357 individuals, whereas the 6 chloroplast gene markers revealed three subpopulations among 160 accessions in the STRUCTURE analysis. In the clustering analysis, the three inbred species clustered into a single group, whereas the outbreeding species were clearly divided, especially according to nuclear SSR markers. In addition, almost all Lolium multiflorum populations were clustered into group C4, which could be further divided into three subgroups, whereas Lolium perenne populations primarily clustered into two groups (C2 and C3), with a few lines that instead grouped with L. multiflorum (C4) or Lolium rigidum (C6). Together, these results will useful for the use of Lolium germplasm for improvement and increase the effectiveness of ryegrass breeding.
Highlights
The genus Lolium comprises nine species representing both outbreeding and inbreeding species (Terrell, 1968; Scholz et al, 2000), of which the most commonly used species are Lolium perenne L. and Lolium multiflorum L. (Italian ryegrass or annual ryegrass)
simple sequence repeat (SSR) marker were transferred between Festuca–Lolium complex (Rouf Mian et al, 2005; Hirata et al, 2006, 2011; Kirigwi et al, 2008; Sharifi Tehrani et al, 2008; Hand et al, 2012), in this study, SSR markers form Italian ryegrass were used, in our results, the 32 nuclear SSR markers were successfully amplified in all nine Lolium species used, and showed higher genetic diversity and polymorphism information content (PIC)-values in out-crossing species than inbreeding species, suggesting the usefulness of these SSR markers in Lolium genetic diversity study
We have tested a total of 38 primer pairs from chloroplast genes and 30 primer pairs from mitochondrial genes designed from rice and other species, and almost all the primers could provide single clear amplification products in Italian ryegrass (Cai et al, 2009)
Summary
The genus Lolium comprises nine species representing both outbreeding and inbreeding species (Terrell, 1968; Scholz et al, 2000), of which the most commonly used species are Lolium perenne L. (perennial ryegrass) and Lolium multiflorum L. (Italian ryegrass or annual ryegrass). Most studies have indicated that the genus can be divided into two groups—an inbreeding group and an outbreeding group—according to morphologic features (Bulinska-Radomska and Lester, 1985; Loos, 1993; Bennett et al, 2000), seed proteins (BulinskaRadomska and Lester, 1985), isozymes and interspecific hybridization (Charmet and Balfourier, 1994; Charmet et al, 1996), and molecular markers such as restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers (Charmet et al, 1997), internal transcribed spacer (ITS) rDNA (Charmet et al, 1997; Gaut et al, 2000; Catalan et al, 2004), sequence-related amplified polymorphism (SRAP) markers (Cheng et al, 2016a), and chloroplast DNA (Balfourier et al, 2000; Cheng et al, 2016b) Both L. rigidum and L. perenne are outbreeding species, among 51 natural populations sampled throughout Europe and the Middle East, most of the L. rigidum populations clustered with those of the three inbred species (L. temulentum, L. persicum, and L. remotum), whereas the L. perenne populations could be divided between two different clusters on the basis of chloroplast DNA markers (Balfourier et al, 2000). Both L. rigidum and L. perenne are outbreeding species, among 51 natural populations sampled throughout Europe and the Middle East, most of the L. rigidum populations clustered with those of the three inbred species (L. temulentum, L. persicum, and L. remotum), whereas the L. perenne populations could be divided between two different clusters on the basis of chloroplast DNA markers (Balfourier et al, 2000). Cresswell et al (2001) used amplified fragment length polymorphism (AFLP) markers to analyze three populations of L. perenne, four of L. multiflorum, and nine of their hybrid, L. × hybridum, from locations across Portugal and found that the three populations of L. perenne formed a discrete cluster that was widely separated from all other populations, whereas, L. × hybridum populations formed two distinct groups, one of which was similar to and overlapped with L. multiflorum, and the second formed a separate cluster
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