Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan

Abdel‐Ghani, Adel H.; Parzies, Heiko K.; Omary, Ayed; Geiger, H. H.

doi:10.1007/s00122-004-1657-1

Cited by 93 publications

(83 citation statements)

References 44 publications

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“…More xeric sites had a higher self-fertilization rate than mesic sites, with average rates of 99.6 and 97.9%, respectively. A recent study of 12 populations in Jordan that employed microsatellitebased estimates of outcrossing rate reported an average selfing rate of 99.7% (Abdel-Ghani et al 2004). Reports of observed heterozygosity based on numerous studies of allelic diversity in wild barley are consistent in suggesting very high rates of self-fertilization (cf.…”

Section: Discussionmentioning

confidence: 96%

Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic Diversity

et al. 2006

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Recombination occurs through both homologous crossing over and homologous gene conversion during meiosis. The contribution of recombination relative to mutation is expected to be dramatically reduced in inbreeding organisms. We report coalescent-based estimates of the recombination parameter (r) relative to estimates of the mutation parameter (u) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp. spontaneum. Estimates of r/u are much greater than expected, with a meanr/û % 1.5, similar to estimates from outcrossing species. We also estimater with and without the contribution of gene conversion. Genotyping errors can mimic the effect of gene conversion, upwardly biasing estimates of the role of conversion. Thus we report a novel method for identifying genotyping errors in nucleotide sequence data sets. We show that there is evidence for gene conversion in many large nucleotide sequence data sets including our data that have been purged of all detectable sequencing errors and in data sets from Drosophila melanogaster, D. simulans, and Zea mays. In total, 13 of 27 loci show evidence of gene conversion. For these loci, gene conversion is estimated to contribute an average of twice as much as crossing over to total recombination. T HERE are two sources of genetic diversity, mutation and recombination. Mutation, broadly defined here as novel heritable change in nucleotide state, introduces new variants while recombination reassorts the variants along a chromosome into novel combinations or haplotypes. Recombination can occur through both homologous crossover and homologous (intralocus) gene conversion, processes that occur as part of meiosis in diploid (or higher ploidy) organisms (Wiuf and Hein 2000). Under the Holliday junction model (Holliday 1964), homologous gene conversion is thought to occur when only a short tract of the alternate chromosome (usually a few hundred base pairs) is incorporated during meiotic exchange (e.g., Stahl 1994).Inbreeding dramatically reduces the role of recombination. Recurrent inbreeding can rapidly increase homozygosity; the recombination process continues to exchange chromosomal segments during gamete formation but with little effective recombination of mutations. Thus the primary impact of inbreeding is expected to be a reduction of the contribution of recombination, relative to mutation, to total genetic diversity.Under coalescent theory and assuming a standard neutral model, the impact of inbreeding can be measured as a reduction in the ratio of the recombination parameter r to the mutation parameter u, i.e., r/u (where r ¼ 4N e r and u ¼ 4N e m and where N e is the effective population size, r is the rate of recombination, and m is the rate of mutation) (symbols used are listed in Table 1). It is predicted that both r and u are reduced by inbreeding, but the impact on recombination is expected to be much greater (Nordborg 2000). Nordborg (2000) showed that r is predicted to be reduced under partial self-fertilization based on the relat...

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Section: Discussionmentioning

confidence: 96%

Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic Diversity

et al. 2006

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“…Our data suggested that under certain, currently unknown, circumstances, pollen flow may become substantial as evidenced by high observed heterozygosity in the BG population. Other studies have indicated that high annual precipitation and cool temperature during flowering time may enhance outcrossing in wild barley (Brown et al, 1978b;Abdel-Ghani et al, 2004).…”

Section: Discussion Sgs In a Predominant Selfermentioning

confidence: 98%

Fine-scale spatial genetic structure in a predominantly selfing plant: role of seed and pollen dispersal

2009

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We present a study of fine-scale spatial genetic structure (SGS) and assess the impact of seed and pollen dispersal on the pattern of genetic diversity in the predominantly selfing Hordeum spontaneum. The study included (1) direct measurement of dispersal in a controlled environment, and (2) analyses of SGS and estimation of the ratio of pollen to seed flow in three natural populations sampled in linear transects at fixed increasing inter-plant distances. Analysis of SGS with 10 nuclear SSRs showed in all three populations a significant autocorrelation for the distance classes of 1 or 2 m and a negative linear relationship between kinship coefficients, calculated for pairs of individuals, and logarithm of geographical distance between members of the pairs. Major seed dispersal (95%) was found to be within 1.2 m from the mother plant. Pollen flow, estimated from the comparison of nuclear and chloroplast variation, was spatially limited as much as was seed dispersal, and tended to be overestimated when measured at spatial scales exceeding that of SGS. We conclude that combined effects of selfing, occasional outcrossing, localized seed dispersal and high plant density create an equilibrium between drift and gene flow in this species resulting in SGS at a very fine spatial scale.

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“…Extensive genotypic analysis of diverse germplasm has revealed that restricted outcrossing (0-1.8%) 43 , combined with low recombination in pericentromeric regions, has resulted in modern germplasm that shows limited regional haplotype diversity 44 . We investigated the frequency and distribution of genome diversity by survey sequencing four diverse barley cultivars ('Bowman', 'Barke', 'Igri' and 'Haruna Nijo') and an H. spontaneum accession (Methods and Supplementary Note 8) to a depth of 5-25-fold coverage, and mapping sequence reads against the barley cultivar 'Morex' gene space.…”

Section: Natural Diversitymentioning

confidence: 99%

A physical, genetic and functional sequence assembly of the barley genome

2012

Nature

1,293

880

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Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement

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Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan

Cited by 93 publications

References 44 publications

Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic Diversity

Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic Diversity

Fine-scale spatial genetic structure in a predominantly selfing plant: role of seed and pollen dispersal

A physical, genetic and functional sequence assembly of the barley genome

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