Journal articles 2014
Documents
A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies
Ruperao P, Chan CKK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J, Chitikineni A, Visendi P, Gaur PM, Millán T, Singh KB, Taran B, Wang J, Batley J, Doležel J, Varshney RK and Edwards D (2014). A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 12:778–786 (DOI: 10.1111/pbi.12182). Not open access; view abstract.
Ruperao P, Chan CKK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J, Chitikineni A, Visendi P, Gaur PM, Millán T, Singh KB, Taran B, Wang J, Batley J, Doležel J, Varshney RK and Edwards D (2014). A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal 12:778–786 (DOI: 10.1111/pbi.12182). Not open access; view abstract.
A SSR kit to study genetic diversity in chickpea (Cicer arietinum L.)
Varshney RK, Thudi M, Upadhyaya H, Dwivedi S, Udupa S, Furman B, Baum M and Hoisington D (2014). A SSR kit to study genetic diversity in chickpea (Cicer arietinum L.). Plant Genetic Resources 12(S):S118–S120 (DOI: 10.1017/S1479262114000392). Not open access; view abstract.
Varshney RK, Thudi M, Upadhyaya H, Dwivedi S, Udupa S, Furman B, Baum M and Hoisington D (2014). A SSR kit to study genetic diversity in chickpea (Cicer arietinum L.). Plant Genetic Resources 12(S):S118–S120 (DOI: 10.1017/S1479262114000392). Not open access; view abstract.
Although drought intensity increases aflatoxin contamination, drought tolerance does not lead to less aflatoxin contamination
Hamidou F, Rathore A, Waliyar F and Vadez V (2014). Although drought intensity increases aflatoxin contamination, drought tolerance does not lead to less aflatoxin contamination. Field Crops Research 156:103–110 (DOI: 10.1016/j.fcr.2013.10.019).
Highlights:
- Groundnut germplasm was assessed across varying drought intensities.
- Drought intensity increased aflatoxin concentration in seeds.
- Across trials aflatoxin concentration and grain yield reduction were highly correlated.
- However within trial, aflatoxin and grain yield reduction were unrelated, showing no direct relationship between drought tolerance and resistance to aflatoxin contamination.
- Mechanisms of drought tolerance and aflatoxin contamination are likely not common.
Abstract: Drought stress is known to increase aflatoxin contamination in groundnut and establishing a possible relationship between drought tolerance and resistance to aflatoxin contamination could contribute to a more efficient selection of aflatoxin-resistant genotypes. In recent work, the reference collection of groundnut had been assessed across seasons varying for drought intensity, i.e. two moderate temperature (rainy season) and two high temperature (dry season) experiments under well-watered (WW) and water stress (WS) conditions (Hamidou et al., 2012 and Hamidou et al., 2013). Here aflatoxin concentration (AC) in seeds is measured in these trials, first for possibly identifying germplasm with low aflatoxin concentrations and second for investigating possible relationships between aflatoxin concentration and drought tolerance. Drought stress intensity increased aflatoxin concentration in seeds and higher aflatoxin contamination was observed under combined drought and high temperature conditions than under drought alone. No germplasm with lower AC than resistant check (55-437) were found. Aflatoxin contamination showed very high GxE interactions, which suggest that selection for resistance to aflatoxin contamination must be specific to environment. Across trials, using means for each environment, there was a clear positive relationship between the aflatoxin concentration and the grain yield reduction due to drought, indicating that a higher drought severity led to higher aflatoxin concentration. However, within trial, the same relationships applied to individual genotypes, or to cohorts of tolerant/sensitive genotypes, were not significant. The major conclusion of this work is that while drought intensity did increase the level of aflatoxin contamination, as expected and previously reported, there seemed to be no direct relationship between tolerance to drought and aflatoxin concentration, suggesting that the mechanisms of drought tolerance and aflatoxin contamination are likely not common.
Hamidou F, Rathore A, Waliyar F and Vadez V (2014). Although drought intensity increases aflatoxin contamination, drought tolerance does not lead to less aflatoxin contamination. Field Crops Research 156:103–110 (DOI: 10.1016/j.fcr.2013.10.019).
Highlights:
- Groundnut germplasm was assessed across varying drought intensities.
- Drought intensity increased aflatoxin concentration in seeds.
- Across trials aflatoxin concentration and grain yield reduction were highly correlated.
- However within trial, aflatoxin and grain yield reduction were unrelated, showing no direct relationship between drought tolerance and resistance to aflatoxin contamination.
- Mechanisms of drought tolerance and aflatoxin contamination are likely not common.
Abstract: Drought stress is known to increase aflatoxin contamination in groundnut and establishing a possible relationship between drought tolerance and resistance to aflatoxin contamination could contribute to a more efficient selection of aflatoxin-resistant genotypes. In recent work, the reference collection of groundnut had been assessed across seasons varying for drought intensity, i.e. two moderate temperature (rainy season) and two high temperature (dry season) experiments under well-watered (WW) and water stress (WS) conditions (Hamidou et al., 2012 and Hamidou et al., 2013). Here aflatoxin concentration (AC) in seeds is measured in these trials, first for possibly identifying germplasm with low aflatoxin concentrations and second for investigating possible relationships between aflatoxin concentration and drought tolerance. Drought stress intensity increased aflatoxin concentration in seeds and higher aflatoxin contamination was observed under combined drought and high temperature conditions than under drought alone. No germplasm with lower AC than resistant check (55-437) were found. Aflatoxin contamination showed very high GxE interactions, which suggest that selection for resistance to aflatoxin contamination must be specific to environment. Across trials, using means for each environment, there was a clear positive relationship between the aflatoxin concentration and the grain yield reduction due to drought, indicating that a higher drought severity led to higher aflatoxin concentration. However, within trial, the same relationships applied to individual genotypes, or to cohorts of tolerant/sensitive genotypes, were not significant. The major conclusion of this work is that while drought intensity did increase the level of aflatoxin contamination, as expected and previously reported, there seemed to be no direct relationship between tolerance to drought and aflatoxin concentration, suggesting that the mechanisms of drought tolerance and aflatoxin contamination are likely not common.
Full article
An Integrated SNP Mining and Utilization (ISMU) pipeline for next generation sequencing data
Azam S, Rathore A, Shah TM, Telluri M, Amindala B, Ruperao P, Katta MAVS and Varshney RK (2014). An Integrated SNP Mining and Utilization (ISMU) pipeline for next generation sequencing data. PLoS ONE 9(7):e101754 (DOI:10.1371/journal.pone.0101754).
Abstract: Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software.
Azam S, Rathore A, Shah TM, Telluri M, Amindala B, Ruperao P, Katta MAVS and Varshney RK (2014). An Integrated SNP Mining and Utilization (ISMU) pipeline for next generation sequencing data. PLoS ONE 9(7):e101754 (DOI:10.1371/journal.pone.0101754).
Abstract: Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software.
Assessment of irrigation scenarios to improve performances of Lingot bean (Phaseolus vulgaris) in southwest France
Marrou H, Sinclair TR and Metral R (2014). Assessment of irrigation scenarios to improve performances of Lingot bean (Phaseolus vulgaris) in southwest France. European Journal of Agronomy 59:22–28 (DOI: 10.1016/j.eja.2014.05.006). Not open access; view abstract. (G6010.05)
Marrou H, Sinclair TR and Metral R (2014). Assessment of irrigation scenarios to improve performances of Lingot bean (Phaseolus vulgaris) in southwest France. European Journal of Agronomy 59:22–28 (DOI: 10.1016/j.eja.2014.05.006). Not open access; view abstract. (G6010.05)
Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB
Caniato FF, Hamblin MT, Guimaraes CT, Zhang Z, Schaffert RE, Kochian LV and Magalhaes JV (2014). Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB. PLoS ONE 9(1):e87438 (DOI: 10.1371/journal.pone.0087438).
Abstract: Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, AltSB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the AltSB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within AltSB. A haplotype network analysis suggested a single geographic and racial origin of causative mutations in primordial guinea domesticates in West Africa. Al tolerance assessment in accessions harboring recombinant haplotypes suggests that causative polymorphisms are localized to a ~6 kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. The SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to lead to the efficient identification, in diverse sorghum germplasm, of Al tolerant accessions able maintain grain yields under Al toxicity.
Caniato FF, Hamblin MT, Guimaraes CT, Zhang Z, Schaffert RE, Kochian LV and Magalhaes JV (2014). Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB. PLoS ONE 9(1):e87438 (DOI: 10.1371/journal.pone.0087438).
Abstract: Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, AltSB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the AltSB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within AltSB. A haplotype network analysis suggested a single geographic and racial origin of causative mutations in primordial guinea domesticates in West Africa. Al tolerance assessment in accessions harboring recombinant haplotypes suggests that causative polymorphisms are localized to a ~6 kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. The SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to lead to the efficient identification, in diverse sorghum germplasm, of Al tolerant accessions able maintain grain yields under Al toxicity.
Bulk genetic characterization of Ghanaian maize landraces using microsatellite markers
Oppong A, Bedoya CA, Ewool MB, Asante MD, Thompson RN, Adu-Dapaah H, Lamptey JNL, Ofori K, Offei SK and Warburton ML (2014). Bulk genetic characterization of Ghanaian maize landraces using microsatellite markers. Maydica 59:1–8. (G4007.13.04)
Abstract: Maize (Zea mays L) was first introduced into Ghana over five centuries ago and remains the most important cereal staple, grown in all agro-ecologies across the country. Yield from farmers' fields are low, which is attributed in part to farmer's preferences and/or reliance on local landraces for cultivation. Efforts are underway to improve some of these landraces for improved productivity. Seeds of maize landraces cultivated in all agro-ecologies were collected for genetic characterization using a bulked fingerprinting technique and 20 SSR markers. In all, 20 populations of 15 plants each from Ghana and 4 control populations from Latin America were characterized. The cluster analysis grouped the 20 landraces into two major groups corresponding to the vegetation/climatic conditions of the north and south of the country. Genotypes from Ashanti, which is centrally located, fell into both major clusters, which suggest its importance in maize seed distribution in Ghana and also the diverse climate/vegetation. Structure analyses grouped the genotypes into two major clusters similar to the UPGMA cluster, and populations were not fully distinct according to F statistics. The results suggest that breeders should make performance data available to seed dealers for better productivity.
Oppong A, Bedoya CA, Ewool MB, Asante MD, Thompson RN, Adu-Dapaah H, Lamptey JNL, Ofori K, Offei SK and Warburton ML (2014). Bulk genetic characterization of Ghanaian maize landraces using microsatellite markers. Maydica 59:1–8. (G4007.13.04)
Abstract: Maize (Zea mays L) was first introduced into Ghana over five centuries ago and remains the most important cereal staple, grown in all agro-ecologies across the country. Yield from farmers' fields are low, which is attributed in part to farmer's preferences and/or reliance on local landraces for cultivation. Efforts are underway to improve some of these landraces for improved productivity. Seeds of maize landraces cultivated in all agro-ecologies were collected for genetic characterization using a bulked fingerprinting technique and 20 SSR markers. In all, 20 populations of 15 plants each from Ghana and 4 control populations from Latin America were characterized. The cluster analysis grouped the 20 landraces into two major groups corresponding to the vegetation/climatic conditions of the north and south of the country. Genotypes from Ashanti, which is centrally located, fell into both major clusters, which suggest its importance in maize seed distribution in Ghana and also the diverse climate/vegetation. Structure analyses grouped the genotypes into two major clusters similar to the UPGMA cluster, and populations were not fully distinct according to F statistics. The results suggest that breeders should make performance data available to seed dealers for better productivity.
Cassava genome from a wild ancestor to cultivated varieties
Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, Lindberg Møller B, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJCB, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, Jørgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, Becerra López-Lavalle LA, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K and Peng M (2014). Cassava genome from a wild ancestor to cultivated varieties. Nature Communications 5:5110 (DOI: 10.1038/ncomms6110). (G3007.03)
Abstact: Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line.We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
Wang W, Feng B, Xiao J, Xia Z, Zhou X, Li P, Zhang W, Wang Y, Lindberg Møller B, Zhang P, Luo MC, Xiao G, Liu J, Yang J, Chen S, Rabinowicz PD, Chen X, Zhang HB, Ceballos H, Lou Q, Zou M, Carvalho LJCB, Zeng C, Xia J, Sun S, Fu Y, Wang H, Lu C, Ruan M, Zhou S, Wu Z, Liu H, Kannangara RM, Jørgensen K, Neale RL, Bonde M, Heinz N, Zhu W, Wang S, Zhang Y, Pan K, Wen M, Ma PA, Li Z, Hu M, Liao W, Hu W, Zhang S, Pei J, Guo A, Guo J, Zhang J, Zhang Z, Ye J, Ou W, Ma Y, Liu X, Tallon LJ, Galens K, Ott S, Huang J, Xue J, An F, Yao Q, Lu X, Fregene M, Becerra López-Lavalle LA, Wu J, You FM, Chen M, Hu S, Wu G, Zhong S, Ling P, Chen Y, Wang Q, Liu G, Liu B, Li K and Peng M (2014). Cassava genome from a wild ancestor to cultivated varieties. Nature Communications 5:5110 (DOI: 10.1038/ncomms6110). (G3007.03)
Abstact: Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line.We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
Cluster analysis of the main agronomic traits of 30 spring wheat strains
Wang H, Shi Y, Ma H, Dong F and Sun D (2014) Cluster analysis of the main agronomic traits of 30 spring wheat strains. Chinese Agricultural Science Bulletin 30(18):60−64. Article in Chinese with abstract in English. Not open access; view journal website. (G7010.02.01)
Wang H, Shi Y, Ma H, Dong F and Sun D (2014) Cluster analysis of the main agronomic traits of 30 spring wheat strains. Chinese Agricultural Science Bulletin 30(18):60−64. Article in Chinese with abstract in English. Not open access; view journal website. (G7010.02.01)
Common beans, biodiversity, and multiple stresses: Challenges of drought resistance in tropical soils
Beebe SE, Rao IM, Devi MJ and Polania J (2014). Common beans, biodiversity, and multiple stresses: Challenges of drought resistance in tropical soils. Crop and Pasture Science 65(7):667–675 (DOI: 10.1071/CP13303). Not open access; view abstract.
Beebe SE, Rao IM, Devi MJ and Polania J (2014). Common beans, biodiversity, and multiple stresses: Challenges of drought resistance in tropical soils. Crop and Pasture Science 65(7):667–675 (DOI: 10.1071/CP13303). Not open access; view abstract.
