Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass

Brazauskas, Gintaras; Lenk, Ingo; Pedersen, Morten Greve; Studer, Bruno; Lübberstedt, Thomas

doi:10.1016/j.plantsci.2011.06.013

Cited by 38 publications

(52 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For the SSR markers, 8.4 alleles per locus were found on average, which is lower than the 9.9 [43], 13.3 [22] and 19.4 [21] found in other studies, even though a much higher number of accessions was examined in our study. The limited number of alleles might be attributed to the usage of bulk samples.…”

Section: Discussioncontrasting

confidence: 92%

See 1 more Smart Citation

DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling

et al. 2018

Self Cite

View full text Add to dashboard Cite

BackgroundLolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. However, improvement in biomass yield has been limited by comparison with other major crops. More efficient utilisation of genetic resources and improved breeding schemes are required to advance L. perenne breeding. In an attempt to elucidate the extent of genetic diversity in L. perenne, 1384 DArT, 182 SNP and 48 SSR markers were applied to 297 accessions (Set I) contributed by three German breeding companies and the IPK Genebank. Due to the heterogeneous nature of Lolium accessions, bulk samples were used. Apart from germplasm set I, additional set II and set III was used to determine the reproducibility of marker system and judge the feasibility of bulk strategy in this study.ResultsBy assessing different bulk sizes, 24 individuals per sample were shown to be a representative number of plants to discriminate different accessions. Among the 297 accessions, all marker types revealed a high polymorphism rate; 1.99, 2.00 and 8.19 alleles, were obtained per locus on average using DArTs, SNPs and SSRs, respectively. The Jaccard distance for DArT markers ranged from 0.00 to 0.73, the Modified Roger’s distance (MRD) for SNP markers ranged from 0.03 to 0.52, and for SSR markers from 0.26 to 0.76. Gene diversity for dominant DArT and co-dominant SNP and SSR markers was found to be 0.26, 0.32 and 0.45, respectively. DArT markers showed the highest consistency and reproducibility.ConclusionThe resulting data were evaluated using a number of different classification methods, but none of the methods showed a clear differentiation into distinct genetic pools. With regard to hybrid breeding, this will possibly impede substantial progress towards increased biomass yields of L. perenne by utilising heterosis.Electronic supplementary materialThe online version of this article (10.1186/s12863-017-0589-0) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussioncontrasting

confidence: 92%

“…To date, the diversity of various L. perenne germplasm or cultivars has been examined with different molecular marker types including AFLP [14–16], ISSR [17–19], RAPD [8, 20], and SSR [21, 22]. However, the number of examined accessions in these studies was generally limited.…”

Section: Introductionmentioning

confidence: 99%

DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…Alternatively, re-sequencing of candidate genes is an option of choice in species with rapidly decaying LD. Rapid LD decay within 300-2,000 bp has been reported in perennial ryegrass (Xing et al 2007;Brazauskas et al 2011), and several studies have already demonstrated the feasibility of the candidate gene-based association mapping approach in perennial ryegrass. A candidate gene, FLOWERING LOCUS T, was found to be associated with changes in flowering time across a range of populations (Skøt et al 2011).…”

Section: Introductionmentioning

confidence: 96%

Association of single nucleotide polymorphisms in LpIRI1 gene with freezing tolerance traits in perennial ryegrass

et al. 2014

View full text Add to dashboard Cite

Perennial ryegrass is an important agricultural crop, however, it is susceptible to winterkill. Freezing injury is caused primarily by ice formation. The LpIRI1 protein has the potential to inhibit ice recrystallization, thus minimize the damage. An association study was conducted using single nucleotide polymorphisms obtained through allele sequencing of the LpIRI1 gene and phenotypic data were collected using two phenotyping platforms in a perennial ryegrass association mapping population of 76 diverse genotypes. Winter survival (FWS) was evaluated under field conditions, while tiller survival (PTS) and electrolyte leakage (EL) at -8 and -12°C were determined under controlled-environment conditions. Proline content (PC) in cold-acclimated plants was measured prior to the freezing test. Significant variation in FWS, PTS, EL and PC was observed among genotypes in our panel. EL and PTS revealed significant negative correlations at -8°C (r s = -0.40) and -12°C (r s = -0.49). PC, however, did not show significant correlations with any of the measured traits, while FWS was correlated (r s = -0.48) with EL at -12°C. The LpIRI1 gene was found to be highly polymorphic with an average SNP frequency of 1 SNP per 16 bp. Association analysis revealed two non-synonymous SNPs being associated with increased EL, both located in the LpIRI1 leucinerich repeat. The results indicate that allelic variation in the LpIRI1 gene plays an important role in the cell membrane integrity of perennial ryegrass during freezing, and can be exploited for developing more freezing tolerant cultivars.

show abstract

“…Varieties are synthetics, due to biological constraints. In this species, LD decreases very rapidly (r 2 < 0.2 over less than 1 kb) in natural populations but also in synthetic varieties, except for in varieties produced from a very small number of parental plants [9,10]. Leaf length and leaf elongation rate are important traits affecting: (i) vegetative yield [11][12][13][14][15]; (ii) intake rate by dairy cows [16]; and (iii) plant survival under light competition conditions [17].…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Loci (QTL) Identification in the Progeny of a Polycross

Pauly¹,

Flajoulot²,

Garon³

et al. 2016

Agronomy

View full text Add to dashboard Cite

Connected multiparental crosses are valuable for detecting quantitative trait loci (QTL) with multiple alleles. The objective of this study was to show that the progeny of a polycross can be considered as connected mutiparental crosses and used for QTL identification. This is particularly relevant in outbreeding species showing strong inbreeding depression and for which synthetic varieties are created. A total of 191 genotypes from a polycross with six parents were phenotyped for plant height (PH) and plant growth rate (PGR) and genotyped with 82 codominant markers. Markers allowed the identification of the male parent for each sibling and so the 191 genotypes were divided into 15 full-sib families. The number of genotypes per full-sib family varied from 2 to 28. A consensus map of 491 cM was built and QTL were detected with MCQTL-software dedicated to QTL detection in connected mapping populations. Two major QTL for PH and PGR in spring were identified on linkage groups 3 and 4. These explained from 12% to 22% of phenotypic variance. The additive effects reached 12.4 mm for PH and 0.11 mm/C • d for PGR. This study shows that the progenies of polycrosses can be used to detect QTL.

show abstract

Genetic variation, population structure, and linkage disequilibrium in European elite germplasm of perennial ryegrass

Cited by 38 publications

References 42 publications

DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling

DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling

Association of single nucleotide polymorphisms in LpIRI1 gene with freezing tolerance traits in perennial ryegrass

Quantitative Trait Loci (QTL) Identification in the Progeny of a Polycross

Contact Info

Product

Resources

About