Worldwide phylogeography and history of wheat genetic diversity

Since its domestication in the Fertile Crescent ~8000 to 10,000 years ago, wheat has undergone a complex history of spread, adaptation, and selection. To get better insights into the wheat phylogeography and genetic diversity, we describe allele distribution through time using a set of 4506 landraces and cultivars originating from 105 different countries genotyped with a high-density single-nucleotide polymorphism array. Although the genetic structure of landraces is collinear to ancient human migration roads, we observe a reshuffling through time, related to breeding programs, with the appearance of new alleles enriched with structural variations that may be the signature of introgressions from wild relatives after 1960

Evaluation of the genetic variability of homoeologous group 3 SSRs in bread wheat

Thorough characterization of the genetic variability in bread wheat (Triticum aestivum L.) is important for a better improvement of this key crop and to increase cereal yield in the context of sustainable agriculture to face human needs in the next decades. To study the genetic variability of SSRs on wheat homoeologous group 3 chromosomes, we characterized 38 hexaploid and two tetraploid wheat lines using a set of 165 microsatellites that we cytogenetically assigned to the 17 deletion bins for chromosomes group 3.Изучали вариабельность МС-локусов третьей гомеологичной группы хромосом T. aestivum L., осуществили сопоставление изменчивости микросателлитов в дистальных и проксимальных областях хромосом и физическое картирование МС-локусов с помощью делеционных, дителосомных, нуллитетрасомных линий и провели сравнительный анализ вариабельности микросателлитных локусов хромосом 3А, 3B и 3D.Вивчали варіабельність МС-локусів третьої гомеологічної групи хромосом T. aestivum L., здійснили порівняння мінливості мікросателітів у дистальних та проксимальних областях хромосом, а також фізичне картування МС-локусів за допомогою делеційних, дітелосомних, нулітетрасомних ліній та провели порівняльний аналіз варіабельності мікросателітних локусів хромосом 3А, 3B і 3D

THE PGR NETWORKS IN FRANCE: COLLABORATION OF USERS AND THE GENETIC RESOURCE CENTRE ON SMALL GRAIN CEREALS

Plant genetic resources (PGR) have been used in breeding programs for many decades to produce modern varieties by introducing genes of interest, in particular, resistance genes. Nevertheless, these resources remain underestimated if we focus on abiotic stress tolerance or new agricultural techniques, which consider productivity with regard to the environment. In recent years, new users, such as scientists and farmers, have discovered diverse sources of interest for screening and exploiting natural diversity conserved in PGR collections.In the case of the French cereals PGR Network, a share of the responsibility, based on the knowledge and ability of network members, has been decided in order to better promote the use of PGR. The main species of Triticum (wheat), Hordeum (barley), Secale (rye), ×Triticosecale (triticale), Avena (oat) genera and their wild relatives are held in the collection. By combining phenotypic and genotypic data, the whole genetic resource collection has been structured into smaller functional groups of accessions, in order to facilitate the access and meet the increasing number of different requirements for the distribution of adapted samples of accessions.New panels are being processed to give breeders and scientists new useful tools to study, for instance, stress resistance or to develop association studies. All these data obtained from the French small grain cereal Network will be progressively available through the INRA Genetic Resource Website (http://urgi.versailles.inra.fr/siregal/siregal/welcome.do)

High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections

The transcription factor GAMYB is involved in gibberellin signalling in cereal aleurone cells and in plant developmental processes. Nucleotide diversity of HvGAMYB and TaGAMYB was investigated in 155 barley (Hordeum vulgare) and 42 wheat (Triticum aestivum) accessions, respectively. Polymorphisms defined 18 haplotypes in the barley collection and 1, 7 and 3 haplotypes for the A, B, and D genomes of wheat, respectively. We found that (1) Hv- and TaGAMYB genes have identical structures. (2) Both genes show a high level of nucleotide identity (>95%) in the coding sequences and the distribution of polymorphisms is similar in both collections. At the protein level the functional domain is identical in both species. (3) GAMYB genes map to a syntenic position on chromosome 3. GAMYB genes are different in both collections with respect to the Tajima D statistic and linkage disequilibrium (LD). A moderate level of LD was observed in the barley collection. In wheat, LD is absolute between polymorphic sites, mostly located in the first intron, while it decays within the gene. Differences in Tajima D values might be due to a lower selection pressure on HvGAMYB, compared to its wheat orthologue. Altogether our results provide evidence that there have been only few evolutionary changes in Hv- and TaGAMYB. This confirms the close relationship between these species and also highlights the functional importance of this transcription factor

Genetic Diversity and Linkage Disequilibrium in Chinese Bread Wheat (Triticum aestivum L.) Revealed by SSR Markers

Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of <5% were found in the landrace and modern variety gene pools, respectively, indicating greater numbers of rare variants, or likely new alleles, in landraces. Analysis of molecular variance (AMOVA) showed that A genome had the largest genetic differentiation and D genome the lowest. In contrast to genetic diversity, modern varieties displayed a wider average LD decay across the whole genome for locus pairs with r2>0.05 (P<0.001) than the landraces. Mean LD decay distance for the landraces at the whole genome level was <5 cM, while a higher LD decay distance of 5–10 cM in modern varieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5∼25 cM) compared to landraces (<5∼15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources

Tracing the ancestry of modern bread wheats

For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world’s most important crops. We use exome sequencing of a worldwide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding has shaped the genetic makeup of modern bread wheats. We observe considerable genetic variation at the genic, chromosomal and subgenomic levels, and use this information to decipher the likely origins of modern day wheats, the consequences of range expansion and the allelic variants selected since its domestication. Our data support a reconciled model of wheat evolution and provide novel avenues for future breeding improvement.</p