Gramene 2016: comparative plant genomics and pathway resources

Tello-Ruiz, Marcela K.; Stein, Joshua C.; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M.; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A.; Huerta, Laura; Keays, Maria; Tang, Y. Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D’Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J.; Jaiswal, Pankaj; Ware, Doreen

doi:10.1093/nar/gkv1179

Cited by 124 publications

(95 citation statements)

References 51 publications

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“…Identification of enzymes involved in N uptake and utilization were retrieved from the SorghumCyc (Tello-Ruiz et al, 2016) and Kyoto Encyclopedia of Genes and Genomes (KEGG) online sorghum pathway database (Kanehisa et al, 2012). Ammonium and nitrate uptake and transporter genes described by von Wittgenstein et al (2014) and Léran et al (2014) were added for analysis.…”

Section: Methodsmentioning

confidence: 99%

Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

Massel

Campbell

Mace³

et al. 2016

Front. Plant Sci.

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Nitrogen (N) fertilizers are a major agricultural input where more than 100 million tons are supplied annually. Cereals are particularly inefficient at soil N uptake, where the unrecovered nitrogen causes serious environmental damage. Sorghum bicolor (sorghum) is an important cereal crop, particularly in resource-poor semi-arid regions, and is known to have a high NUE in comparison to other major cereals under limited N conditions. This study provides the first assessment of genetic diversity and signatures of selection across 230 fully sequenced genes putatively involved in the uptake and utilization of N from a diverse panel of sorghum lines. This comprehensive analysis reveals an overall reduction in diversity as a result of domestication and a total of 128 genes displaying signatures of purifying selection, thereby revealing possible gene targets to improve NUE in sorghum and cereals alike. A number of key genes appear to have been involved in selective sweeps, reducing their sequence diversity. The ammonium transporter (AMT) genes generally had low allelic diversity, whereas a substantial number of nitrate/peptide transporter 1 (NRT1/PTR) genes had higher nucleotide diversity in domesticated germplasm. Interestingly, members of the distinct race Guinea margaritiferum contained a number of unique alleles, and along with the wild sorghum species, represent a rich resource of new variation for plant improvement of NUE in sorghum.

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Section: Methodsmentioning

confidence: 99%

Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

Massel

Campbell

Mace³

et al. 2016

Front. Plant Sci.

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“…Eighty-two selected SSR markers, attributed across the genome linked with amylose content QTL traits, were used to evaluate genetic diversity among rice germplasms. Primer sequences, annealing temperature and chromosomal location information were obtained from GRAMENE database [26]. PCR was performed by using Thermal Cycler GenAtlas S machine (ASTEC Co., Ltd, Fukuoka, Japan) with a total volume of 10 µL of the mixture containing 0.5 µL of template DNA (100 ng), 1 µL of 10× PCR buffer, 0.8 µL of 25 mM MgCl 2 , 0.1 µL of 1 mM dideoxynucleotides (dNTPs), 0.5 µL of 5 µM reverse and forward primers, and 0.05 µL of 0.5 units Taq DNA polymerase.…”

Section: Pcr Amplificationmentioning

confidence: 99%

Identification of Phenotypic Variation and Genetic Diversity in Rice (Oryza sativa L.) Mutants

Anh

Khanh

Dat³

et al. 2018

Agriculture

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Abstract:In this study, phenotypic variation and genetic diversity, important factors to decide germplasm for rice breeding, were evaluated among 15 rice mutants attained from the MNU (N-Nitroso-N-methylurea) mutation. The correlation coefficient values among these phenotypic characteristics were calculated. The results showed that full grain number per plant was the most relevant factor contributing to grain yield per plant, and grain length to width ratio was the key parameter affected to amylose content. Furthermore, the genetic variation among mutants was estimated by Simple Sequence Repeat (SSR) markers related to amylose content trait. Fifty-six polymorphism markers covering across eleven rice chromosomes were recorded with an average of 3.02 alleles per locus. The average value of polymorphism information content was 0.47. By using the unweighted pair group method with arithmetic mean (UPGMA) clustering, four clusters were generated with the genetic similarities ranging from 0.52 to 0.91. The variation among groups was 34%, while the variation among individuals within groups was 66%. Findings of this study provided useful genetic background and phenotypic information of collected rice mutants to breed rice cultivars with improved quality.

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“…The best choice would have been to split them according to exon ranking [37]. However, as exon annotation was lacking (or imprecise) for most species in our datasets, we split contigs into two sets: the first 252 base pairs, corresponding to the median length of the first exon in Arabidopsis, banana and rice (Gramene database [56]), used as a proxy for the first exon, and the rest of the contig. We then estimated B on these two sets of contigs.…”

Section: Variation Along Genesmentioning

confidence: 99%

Evolutionary forces affecting synonymous variations in plant genomes

Clément

Sarah

Homa

et al. 2016

Preprint

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Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.PLOS Genetics | https://doi.org/10.1371/journal.pgen

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Gramene 2016: comparative plant genomics and pathway resources

Cited by 124 publications

References 51 publications

Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

Identification of Phenotypic Variation and Genetic Diversity in Rice (Oryza sativa L.) Mutants

Evolutionary forces affecting synonymous variations in plant genomes

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