Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection

Quraishi, Umar Masood; Abrouk, Michaël; Bolot, Stéphanie; Pont, Caroline; Throude, Mickaël; Guilhot, Nicolas; Confolent, Carole; Bortolini, Fernanda; Praud, Sébastien; Murigneux, Alain; Charmet, Gilles; Salse, Jérôme

doi:10.1007/s10142-009-0129-8

Cited by 89 publications

(76 citation statements)

References 43 publications

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“…Recent advances in comparative sequence analysis between wheat and rice genomes have confirmed extensive synteny between the two species (Sorrells et al, 2003;Quraishi et al, 2009). This enables us to assess the positional correspondence between QTL identified in wheat and known QTL or loci that affect grain morphology in rice.…”

Section: Discussionmentioning

confidence: 96%

A Genetic Framework for Grain Size and Shape Variation in Wheat

et al. 2010

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Grain morphology in wheat (Triticum aestivum) has been selected and manipulated even in very early agrarian societies and remains a major breeding target. We undertook a large-scale quantitative analysis to determine the genetic basis of the phenotypic diversity in wheat grain morphology. A high-throughput method was used to capture grain size and shape variation in multiple mapping populations, elite varieties, and a broad collection of ancestral wheat species. This analysis reveals that grain size and shape are largely independent traits in both primitive wheat and in modern varieties. This phenotypic structure was retained across the mapping populations studied, suggesting that these traits are under the control of a limited number of discrete genetic components. We identified the underlying genes as quantitative trait loci that are distinct for grain size and shape and are largely shared between the different mapping populations. Moreover, our results show a significant reduction of phenotypic variation in grain shape in the modern germplasm pool compared with the ancestral wheat species, probably as a result of a relatively recent bottleneck. Therefore, this study provides the genetic underpinnings of an emerging phenotypic model where wheat domestication has transformed a long thin primitive grain to a wider and shorter modern grain.

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Section: Discussionmentioning

confidence: 96%

A Genetic Framework for Grain Size and Shape Variation in Wheat

et al. 2010

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“…However, despite the relatively low transferability, approximately 40% of the 1,162 orchardgrass SSR primers still showed clear amplification products in the Table 3 Orchardgrass SSR markers used for molecular characterization of subspecies, location of their associated rice homolog, total number of bands detected across 18 accessions and cultivars of orchardgrass, and average number of bands per plant Festuca and Lolium species. These conserved markers provide several hundred primers for comparative genomics, development of conserved orthologous (COS) markers as has been done in Triticeae (Quraishi et al 2009), and functional genetics among these related forage-grass species. Approximately 7% of unigenes contained SSR markers given the parameters we designed (Table 2).…”

Section: Discussionmentioning

confidence: 99%

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

et al. 2011

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Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.

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“…Accurate genetic maps that included the mrs1 gene (Dobrovolskaya et al, 2009) were used for further synteny-based identification of SS candidate markers using the COS genes available in bread wheat (Quraishi et al, 2009;Pont et al, 2013). The mrs1 locus is flanked by the COS1 (LOCOs07g38530-Bradi1g23970-Sb02g037070), COS2 (LOCOs07g45064), and COS3 (LOCOs07g48200-Bradi1g17680-Sb02g043000) markers ( Fig.…”

Section: Dissection Of the Fzp Locus And Identification Of The Gene Imentioning

confidence: 99%

FRIZZY PANICLE Drives Supernumerary Spikelets in Bread Wheat

et al. 2014

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and Central Siberian Botanical Garden, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (A.A.K.) Bread wheat (Triticum aestivum) inflorescences, or spikes, are characteristically unbranched and normally bear one spikelet per rachis node. Wheat mutants on which supernumerary spikelets (SSs) develop are particularly useful resources for work towards understanding the genetic mechanisms underlying wheat inflorescence architecture and, ultimately, yield components. Here, we report the characterization of genetically unrelated mutants leading to the identification of the wheat FRIZZY PANICLE (FZP) gene, encoding a member of the APETALA2/Ethylene Response Factor transcription factor family, which drives the SS trait in bread wheat. Structural and functional characterization of the three wheat FZP homoeologous genes (WFZP) revealed that coding mutations of WFZP-D cause the SS phenotype, with the most severe effect when WFZP-D lesions are combined with a frameshift mutation in WFZP-A. We provide WFZPbased resources that may be useful for genetic manipulations with the aim of improving bread wheat yield by increasing grain number.

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Genomics in cereals: from genome-wide conserved orthologous set (COS) sequences to candidate genes for trait dissection

Cited by 89 publications

References 43 publications

A Genetic Framework for Grain Size and Shape Variation in Wheat

A Genetic Framework for Grain Size and Shape Variation in Wheat

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

FRIZZY PANICLE Drives Supernumerary Spikelets in Bread Wheat

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