Legume comparative genomics: progress in phylogenetics and phylogenomics

Cronk, Quentin; Ojeda, Isidro; Pennington, R. Toby

doi:10.1016/j.pbi.2006.01.011

Cited by 69 publications

(53 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Considering non-CNL-encoding genes, extensive gene collinearity was observed across the legume family, confirming previous syntenic relationships such as between parts of Lj2 and Mt6 (Zhu et al, 2005;Cannon et al, 2006). Considering that the most recent common ancestor between Pv, Lj, Gm, and Mt is dated 54 Mya (Lavin et al, 2005;Cronk et al, 2006), the level of microsynteny observed between the four species is remarkable. Interestingly, this collinearity was strictly restricted to non-CNL-encoding genes, suggesting the existence of CNL gene movement.…”

Section: Discussionsupporting

confidence: 79%

A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean

et al. 2009

View full text Add to dashboard Cite

The B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris [Pv]). It is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-CoilNucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution.

show abstract

Section: Discussionsupporting

confidence: 79%

A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean

et al. 2009

View full text Add to dashboard Cite

show abstract

“…Red clover belongs to the inverted repeat-loss clade subfamily Papilionoideae which includes M. truncatula, Pisum sativum (pea), and Vicia faba (faba bean) [Cronk et al, 2006]. It has an allogamous diploid genome (2n = 14; 1C = 440 Mb) that is similar in size to that of L. japonicus and Oryza sativa (430 Mb).…”

mentioning

confidence: 99%

Integration of Linkage and Chromosome Maps of Red Clover (<b><i>Trifolium pratense</i></b> L.)

Kataoka

Hara

Kato

et al. 2012

Cytogenet Genome Res

View full text Add to dashboard Cite

Red clover (Trifolium pratense L.) is a forage legume and an allogamous diploid plant (2n = 14; 440 Mb). Here, we examine the 7 prometaphase chromosomes of red clover using fluorescence in situ hybridization (FISH) with ribosomal RNA sequences, pericentromeric and telomeric repeats, as well as bacterial artificial chromosome (BAC) clones. Position of hybridization signals and chromosome condensation patterns were quantified by the help of the chromosome image analysis system ver. 4.0 (CHIAS IV). Fourteen BAC clones belonging to linkage groups (LG) 1–7 hybridized to individual chromosomes 4, 2, 6, 5, 1, 7, and 3, respectively. Quantitative analysis of FISH mapping and chromosome analysis using CHIAS IV allowed us to construct a quantitative idiogram that constitutes the comprehensive chromosome map of red clover. Chromosomal positions of the 26S rDNA locus were detected at a heterozygous locus on chromosome 6 in the variety HR, and polymorphisms of rDNA loci were observed in other varieties, although chromosomal positions of some BAC clones did not vary among HR and other varieties. These results demonstrate chromosomal collinearity among allogamous red clover varieties. This integration of genetic linkage and quantitative chromosome maps should provide valuable insight into allogamous legume genetics.

show abstract

“…This was further substantiated by one recent phylogenetic analysis of legumes, based on chloroplast maturase K (matK) sequence (Cronk et al, 2006). In particular, the Papilionoideae subfamily, to which crop and model legumes belong, was subdivided into seven informally named clades.…”

Section: Expected Technologiesmentioning

confidence: 87%

Faba Bean

Link

Hanafy

Malenica

et al. 2008

Compendium of Transgenic Crop Plants

View full text Add to dashboard Cite

Vicia faba L. is an old world grain legume, combine harvested for food and feed in Europe, North and East Africa, Asia, and in the northwest of South America. It is an annual, diploid plant ( x = 6), with a large genome (1C ∼ 13 pg of DNA), large seeds (0.3 up to >2 g per seed), and a protein content of about 30%. Being a small agricultural species, a relatively large producer in Europe is the United Kingdom with more than 150000 ha. On the global scale, China is the largest producer (39% of global area of 2.6 million hectares). Important fungal diseases are Botrytis fabae , Ascochyta fabae , and Uromyces viciae‐fabae . Important pests are Aphis fabae and Bruchus rufimanus . Broomrape ( Orobanche crenata ) is an important parasitic weed in the Mediterranean basin and the Nile valley. Traditional breeding is hampered by the partial allogamous, entomophilous reproduction, with degrees of outcrossing between 20% and 75%, depending on the actual genotype and the environment. The faba bean cannot be crossed with related species, and it is known as recalcitrant crop as to in vitro technologies. Agrobacterium ‐mediated transformation of Vicia faba resulted in regeneration of first transgenic plants carrying the aspartate kinse III from E. coli and the 2S‐albumin 8 from sunflower. In addition to the optimization of the regeneration protocol, knowledge gained from the model legumes Medicago truncatula and Lotus japonicus should enable further progress in Vicia faba breeding.

show abstract

Legume comparative genomics: progress in phylogenetics and phylogenomics

Cited by 69 publications

References 29 publications

A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean

A Nomadic Subtelomeric Disease Resistance Gene Cluster in Common Bean

Integration of Linkage and Chromosome Maps of Red Clover (<b><i>Trifolium pratense</i></b> L.)

Faba Bean

Contact Info

Product

Resources

About