Bridging Model and Crop Legumes through Comparative Genomics

Zhu, Hongyan; Choi, Hyunju; Cook, Douglas R.; Shoemaker, Randy C.

doi:10.1104/pp.104.058891

Cited by 252 publications

(172 citation statements)

References 54 publications

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“…In addition, comparative analysis of legume genomes with other nonlegume genomes, such as Arabidopsis, rice, and poplar (Populus spp. ), will advance the discovery of genes important for seed development in flowering plants (Graham et al, 2004;Zhu et al, 2005). Finally, once a soybean whole-genome GeneChip becomes available, the entire mRNA profiles of all seed and embryo compartments can be determined, completing the identification of seed-and embryo-specific genes.…”

Section: Future Perspectivesmentioning

confidence: 99%

“…The recent development of genomic tools, such as genome sequences, ESTs, oligonucleotide and cDNA microarrays, and comprehensive databases, such as the Legume Information System (http://www.comparative-legumes.org), make legumes an excellent model to study seed development at a global scale (VandenBosch and Stacey, 2003;Gepts et al, 2005;Gonzales et al, 2005). These genomic tools allow comparative genomic analyses in closely related species (Zhu et al, 2005) and should facilitate the identification and investigation of genes important for seed development.…”

Section: Legumes Are An Excellent Model System To Study Seed Developmentmentioning

confidence: 99%

See 1 more Smart Citation

Using Genomics to Study Legume Seed Development

Wagmaister²,

Kawashima³

et al. 2007

Plant Physiology

148

157

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Section: Future Perspectivesmentioning

confidence: 99%

Section: Legumes Are An Excellent Model System To Study Seed Developmentmentioning

confidence: 99%

Using Genomics to Study Legume Seed Development

Wagmaister²,

Kawashima³

et al. 2007

Plant Physiology

148

157

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“…It belongs to the Papilionoideae subfamily Leguminosae, which contains nearly all commercially important crop legumes. The Papilionoideae subfamily falls into two clades, Galegoid and Phaseoloid (Goldblatt 1981;Zhu et al 2005). Soybean is a member of the Phaseoloid clade, together with the common bean (Phaseolus vulgaris) and mungbean (Vigna radiata), whereas the Galegoid clade includes pea (Pisum sativum), alfalfa (Medicago sativa), and two model legumes, Lotus japonicus and Medicago truncatula.…”

mentioning

confidence: 99%

Genetic Redundancy in Soybean Photoresponses Associated With Duplication of the Phytochrome A Gene

et al. 2008

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“…Approximately 33% of human nitrogen requirement is fulfilled by grain legumes as they contain twice the amount of proteins in comparison to cereals [31] and legumes are the single chief dietary source of proteins in many developing countries. They are unique in their capacity for symbiotic nitrogen fixation and thus enhance soil fertility along with serving as an important source of fodder, forage, secondary metabolites and industrial and edible oils.…”

Section: Introductionmentioning

confidence: 99%

Insights into PPR Gene Family in Cajanus Cajan and Other Legume Species

Kaur¹,

Verma²

2016

J Data Mining Genomics Proteomics

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PPR proteins comprises of several hundred members among land plants and govern a fascinating array of functions in organeller genomes that ranges from participation in stabilization of organeller transcripts, RNA editing to fertility restoration of CMS lines. Despite the availability of genome sequences of several legume species, comprehensive cataloguing of members of PPR gene family has not been carried out. In the current study, we identified 523, 830, 534, 816, 441 and 677 PPR proteins in Cajanus, Glycine, Phaseolus, Medicago, Vigna and Cicer genomes, respectively and their complete in silico categorization was undertaken to classify them into various sub-classes and their localization prediction. Chromosomal coordinates of 271 Cajanus PPR genes were predicted and their homologues were identified in 5 other legumes revealing extensive genome conservation. PPR genes of all 6 legume species were further probed to identify restorer of fertility-like PPRs (RFLs) on the basis of protein clustering and followed by homology searches to already known Rf-PPR genes. Seventy RFL PPR genes (P sub-class) were identified and were scrutinized by phylogenetic analysis which revealed extended similarity and common features shared by these RFLs across the species. Some of these RFL PPRs were present as small clusters in Glycine, Phaseolus, Vigna and Cicer genomes. This study has generated a knowledge base about PPR gene family in legumes and opens several avenues for future investigations into their molecular functions, evolutionary relationships and their potential in identifying markers to enable cloning of Rf genes.Citation: Kaur P, Verma M, Chaduvula PK, Saxena S, Baliyan N, et al. (2016) Due to certain limitations of demarking PPR motifs by classical system of categorization, PPR motifs has been redefined by Cheng et al. [15] whereby 10 PPR motif variants have been described and used to annotate PPR sequences in 109 genomes. Newly identified motif variants in PLS sub-class includes P1 and P2 motifs that differ from classical P motif in first helix; S2 (32 amino acid), SS (31 amino acid), E1 (34 amino acid) and E2 (34 amino acid) motif. This revision of PPR classification has provided a clearer picture of PPR structure and thus will provide new insights into their role in molecular and structural evolution.Most of these nuclear encoded PPRs carry N-terminal mitochondrial or chloroplast targeting sequence and are important contributors of various organellar post-transcriptional processes by virtue of their sequence specific RNA binding activity. Considering the array of functions governed by PPR proteins, identification and characterization of homologous and species specific PPR proteins in other plant species is critical for understanding the dynamics of nuclear cytoplasmic interactions.Cytoplasmic male sterility system is widely exploited/ phenomenon for hybrid seed production and has been extensively studied at molecular and biochemical level in various crops. Fertility restorers are an important component o...

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Bridging Model and Crop Legumes through Comparative Genomics

Cited by 252 publications

References 54 publications

Using Genomics to Study Legume Seed Development

Using Genomics to Study Legume Seed Development

Genetic Redundancy in Soybean Photoresponses Associated With Duplication of the Phytochrome A Gene

Insights into PPR Gene Family in Cajanus Cajan and Other Legume Species

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