Journal articles 2013
Documents
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M-C, Thudi M, Gowda CLL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J & Cook DR (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology (2013). (DOI:10.1038/nbt.2491).
Chickpea (Cicer arietinum) is the second most widely grown legume crop after soya bean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.
Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Rosen BD, Tar'an B, Millan T, Zhang X, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M-C, Thudi M, Gowda CLL, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, Singh KB, Datta SK, Jackson SA, Wang J & Cook DR (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nature Biotechnology (2013). (DOI:10.1038/nbt.2491).
Chickpea (Cicer arietinum) is the second most widely grown legume crop after soya bean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ~738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea—desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.
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Drought tolerance in wild plant populations: the case of common beans (Phaseolus vulgaris L.)
Cortés AJ, Monserrate FA, Ramírez-Villegas J, Madriñán S, Blair MW (2013). Drought tolerance in wild plant populations: the case of common beans (Phaseolus vulgaris L.). PLoS ONE 8(5):e62898. (DOI: 10.1371/journal.pone.0062898).
Drought is a major constraint to common bean (Phaseolus vulgaris L.) production, especially in developing countries where irrigation for the crop is infrequent. The Mesoamerican genepool is the most widely grown subdivision of common beans that include small red, small cream and black seeded varieties. The objective of this study was to develop a reliable genetic map for a Mesoamerican 9 Mesoamerican drought tolerant 9 susceptible cross and to use this map to analyze the inheritance of yield traits under drought and fully irrigated conditions over 3 years of experiments. The source of drought tolerance used in the crosswas the cream-seeded advanced line BAT477 crossed with the small red varietyDOR364 and the populationwas made up of recombinant inbred lines in the F5 generation. Quantitative trait loci were detected by composite intervalmapping for the traits of overall seed yield, yield per day, 100 seed weight, days to flowering and days to maturity for each field environment consisting of two treatments (irrigated and rainfed) and lattice design experiments with three repetitions for a total of six environments. The genetic map based on amplified fragment length polymorphism and random amplified polymorphic DNA markers was anchored with 60 simple sequence repeat (SSR) markers and had a total map length of 1,087.5 cM across 11 linkage groups covering the whole common bean genome with saturation of one marker every 5.9 cM. Gaps for the genetic map existed on linkage groups b03, b09 and b11 but overall there were only nine gaps larger than 15 cM. All traits were inherited quantitatively, with the greatest number for seedweight followed by yield per day, yield per se, days to flowering and days to maturity. The relevance of these results for breeding common beans is discussed in particular in the light of crop improvement for drought tolerance in the Mesoamerican genepool.
Cortés AJ, Monserrate FA, Ramírez-Villegas J, Madriñán S, Blair MW (2013). Drought tolerance in wild plant populations: the case of common beans (Phaseolus vulgaris L.). PLoS ONE 8(5):e62898. (DOI: 10.1371/journal.pone.0062898).
Drought is a major constraint to common bean (Phaseolus vulgaris L.) production, especially in developing countries where irrigation for the crop is infrequent. The Mesoamerican genepool is the most widely grown subdivision of common beans that include small red, small cream and black seeded varieties. The objective of this study was to develop a reliable genetic map for a Mesoamerican 9 Mesoamerican drought tolerant 9 susceptible cross and to use this map to analyze the inheritance of yield traits under drought and fully irrigated conditions over 3 years of experiments. The source of drought tolerance used in the crosswas the cream-seeded advanced line BAT477 crossed with the small red varietyDOR364 and the populationwas made up of recombinant inbred lines in the F5 generation. Quantitative trait loci were detected by composite intervalmapping for the traits of overall seed yield, yield per day, 100 seed weight, days to flowering and days to maturity for each field environment consisting of two treatments (irrigated and rainfed) and lattice design experiments with three repetitions for a total of six environments. The genetic map based on amplified fragment length polymorphism and random amplified polymorphic DNA markers was anchored with 60 simple sequence repeat (SSR) markers and had a total map length of 1,087.5 cM across 11 linkage groups covering the whole common bean genome with saturation of one marker every 5.9 cM. Gaps for the genetic map existed on linkage groups b03, b09 and b11 but overall there were only nine gaps larger than 15 cM. All traits were inherited quantitatively, with the greatest number for seedweight followed by yield per day, yield per se, days to flowering and days to maturity. The relevance of these results for breeding common beans is discussed in particular in the light of crop improvement for drought tolerance in the Mesoamerican genepool.
Drought-resistance of local wheat varieties in Shanxi Province of China: A comprehensive evaluation by using GGE biplot and subordinate function
Yang J-W, Zhu J-G, Wang S-G, Sun D-Z, Shi Y-G and Chen W-G (2013). Drought-resistance of local wheat varieties in Shanxi Province of China: A comprehensive evaluation by using GGE biplot and subordinate function. Chinese Journal of Applied Ecology 24(4):1031−1038. (G7010.02.01)
Abstract: Taking 7 local wheat varieties in Shanxi Province of China and two other control varieties as test materials, this paper studied their morphological and physiological traits under normal and water stress field conditions. The drought-resistance coefficient of each index of the traits was calculated. On the basis of principal component analysis, the correlations between the drought-resistance indices and their relationships with the drought-resistance of different varieties were analyzed by GGE biplot, and the drought resistance of the wheat varieties was comprehensively evaluated with the combination of subordinate function and drought resistance index analysis. The main morphological and physiological factors affecting the drought-resistance of the wheat varieties were uppermost internode length, plant height, internode length, leaf area, leaf POD and SOD activities, and leaf relative water content and relative electric conductivity. There existed different degrees of correlation between these indices, and each index had different effects on the drought resistance of the varieties, being the main cause for the different drought resistance of the wheat varieties. Based on the drought-resistance, the test varieties could be classified into three groups, i.e., drought-resistance group, intermediate group, and sensitive group. Two highly drought-resistance cultivars, Baiheshangtou and Zhuganqing, whose drought-resistance was similar to that of drought-resistant Jinmai 47, could be used as the parent materials for breeding drought-resistance wheat.
Yang J-W, Zhu J-G, Wang S-G, Sun D-Z, Shi Y-G and Chen W-G (2013). Drought-resistance of local wheat varieties in Shanxi Province of China: A comprehensive evaluation by using GGE biplot and subordinate function. Chinese Journal of Applied Ecology 24(4):1031−1038. (G7010.02.01)
Abstract: Taking 7 local wheat varieties in Shanxi Province of China and two other control varieties as test materials, this paper studied their morphological and physiological traits under normal and water stress field conditions. The drought-resistance coefficient of each index of the traits was calculated. On the basis of principal component analysis, the correlations between the drought-resistance indices and their relationships with the drought-resistance of different varieties were analyzed by GGE biplot, and the drought resistance of the wheat varieties was comprehensively evaluated with the combination of subordinate function and drought resistance index analysis. The main morphological and physiological factors affecting the drought-resistance of the wheat varieties were uppermost internode length, plant height, internode length, leaf area, leaf POD and SOD activities, and leaf relative water content and relative electric conductivity. There existed different degrees of correlation between these indices, and each index had different effects on the drought resistance of the varieties, being the main cause for the different drought resistance of the wheat varieties. Based on the drought-resistance, the test varieties could be classified into three groups, i.e., drought-resistance group, intermediate group, and sensitive group. Two highly drought-resistance cultivars, Baiheshangtou and Zhuganqing, whose drought-resistance was similar to that of drought-resistant Jinmai 47, could be used as the parent materials for breeding drought-resistance wheat.
Enhancing maize grain yield in acid soils of western Kenya using aluminium tolerant germplasm
Ouma E, Ligeyo D, Matonyei T, Agalo J, Were B, Too E, Onkware A, Gudu S, Kisinyo P and Nyangweso P (2013). Enhancing maize grain yield in acid soils of western Kenya using aluminium tolerant germplasm. Journal of Agricultural Science and Technology A 3:33–46. (ISSN: 1939-1250). (G7010.03.05). Not open access: view abstract
Ouma E, Ligeyo D, Matonyei T, Agalo J, Were B, Too E, Onkware A, Gudu S, Kisinyo P and Nyangweso P (2013). Enhancing maize grain yield in acid soils of western Kenya using aluminium tolerant germplasm. Journal of Agricultural Science and Technology A 3:33–46. (ISSN: 1939-1250). (G7010.03.05). Not open access: view abstract
Evaluation of a collection of rice landraces from Burkina Faso for resistance or tolerance to rice yellow mottle virus
Kam H, Laing MD, Séré Y, Thiémélé D, Ghesquière A, Ahmadi N, Ndjiondjop M-N (2013). Evaluation of a collection of rice landraces from Burkina Faso for resistance or tolerance to rice yellow mottle virus. Journal of Plant Pathology 95(3):485–492 (DOI: 10.4454/JPP.V95I3.014). Not open access; view abstract. (G4009.02.01)
Kam H, Laing MD, Séré Y, Thiémélé D, Ghesquière A, Ahmadi N, Ndjiondjop M-N (2013). Evaluation of a collection of rice landraces from Burkina Faso for resistance or tolerance to rice yellow mottle virus. Journal of Plant Pathology 95(3):485–492 (DOI: 10.4454/JPP.V95I3.014). Not open access; view abstract. (G4009.02.01)
Facing the challenges of global agriculture today: what can we do about drought?
Okono A, Monneveux P and Ribaut J-M (2013). Facing the challenges of global agriculture today: what can we do about drought? Frontiers in Plant Physiology 4:289. (DOI: 10.3389/fphys.2013.00289).
It is estimated that the planet's demand for food and feed crops will almost double by 2050 (Foley et al., 2011). Globally, rainfed agriculture is practised in 80% of the total agricultural area and generates 62% of the world's staple food (FAOSTAT, 2011). Taking into consideration global water scarcity and increases in demand for non-agricultural uses of water, expansion of the area under irrigation in developing countries does not appear to be a realistic scenario to address the challenge of food security.
Okono A, Monneveux P and Ribaut J-M (2013). Facing the challenges of global agriculture today: what can we do about drought? Frontiers in Plant Physiology 4:289. (DOI: 10.3389/fphys.2013.00289).
It is estimated that the planet's demand for food and feed crops will almost double by 2050 (Foley et al., 2011). Globally, rainfed agriculture is practised in 80% of the total agricultural area and generates 62% of the world's staple food (FAOSTAT, 2011). Taking into consideration global water scarcity and increases in demand for non-agricultural uses of water, expansion of the area under irrigation in developing countries does not appear to be a realistic scenario to address the challenge of food security.
Fast-track introgression of “QTL-hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea
Varshney RK, Gaur PM, Chamarthi SK, Krishnamurthy L, Tripathi S, Kashiwagi J, Samineni S, Singh VK, Thudi M, Jaganathan D (2013). Fast-track introgression of “QTL-hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea. The Plant Genome 6(3). (DOI: 10.3835/plantgenome2013.07.0022).
A “QTL-hotspot” containing quantitative trait loci (QTL) for several root and drought tolerance traits was transferred through marker-assisted backcrossing into JG 11, a leading variety of chickpea (Cicer arietinum L.) in India from the donor parent ICC 4958. Foreground selection with up to three simple sequence repeat markers, namely TAA170, ICCM0249, and STMS11, and background selection with up to 10 amplified fragment length polymorphism primer combinations was undertaken. After undertaking three backcrosses with foreground and background selection and selfing, 29 BC3F2 plants homozygous for two markers (ICCM0249 and TAA170) were selected and referred as introgression lines (ILs).
Varshney RK, Gaur PM, Chamarthi SK, Krishnamurthy L, Tripathi S, Kashiwagi J, Samineni S, Singh VK, Thudi M, Jaganathan D (2013). Fast-track introgression of “QTL-hotspot” for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea. The Plant Genome 6(3). (DOI: 10.3835/plantgenome2013.07.0022).
A “QTL-hotspot” containing quantitative trait loci (QTL) for several root and drought tolerance traits was transferred through marker-assisted backcrossing into JG 11, a leading variety of chickpea (Cicer arietinum L.) in India from the donor parent ICC 4958. Foreground selection with up to three simple sequence repeat markers, namely TAA170, ICCM0249, and STMS11, and background selection with up to 10 amplified fragment length polymorphism primer combinations was undertaken. After undertaking three backcrosses with foreground and background selection and selfing, 29 BC3F2 plants homozygous for two markers (ICCM0249 and TAA170) were selected and referred as introgression lines (ILs).
Functional roles of the plasticity of root system development in biomass production and water uptake under rainfed lowland condition
Kano-Nakata M, Gowda VRP, Henry A, Serraj R, Inukai Y, Fujita D, Kobayashi N, Suralta RR, and Yamauchi A (2013). Functional roles of the plasticity of root system development in biomass production and water uptake under rainfed lowland conditions. Field Crops Research 144:288–296. (DOI: 10.1016/j.fcr.2013.01.024). (G3008.06). Not open access: view abstract
Kano-Nakata M, Gowda VRP, Henry A, Serraj R, Inukai Y, Fujita D, Kobayashi N, Suralta RR, and Yamauchi A (2013). Functional roles of the plasticity of root system development in biomass production and water uptake under rainfed lowland conditions. Field Crops Research 144:288–296. (DOI: 10.1016/j.fcr.2013.01.024). (G3008.06). Not open access: view abstract
Genetic Diversity of Cassava (Manihot esculenta Crantz) landraces and cultivars from Southern, Eastern and Central Africa
Kawuki RS, Herselman L, Labuschagne MT, Nzuki I, Ralimanana I, Bidiaka M, Kanyange MC, Gashaka G, Masumba E, Mkamilo G, Gethi J, Wanjala B, Zacarias A, Madabula F and Ferguson ME (2013). Genetic Diversity of Cassava (Manihot esculenta Crantz) landraces and cultivars from Southern, Eastern and Central Africa. Plant Genetic Resources FirstView Article CJO2013, pp 1–12. Published online: 12 February 2013. (DOI: 10.1017/S1479262113000014). Not open access: view abstract
Kawuki RS, Herselman L, Labuschagne MT, Nzuki I, Ralimanana I, Bidiaka M, Kanyange MC, Gashaka G, Masumba E, Mkamilo G, Gethi J, Wanjala B, Zacarias A, Madabula F and Ferguson ME (2013). Genetic Diversity of Cassava (Manihot esculenta Crantz) landraces and cultivars from Southern, Eastern and Central Africa. Plant Genetic Resources FirstView Article CJO2013, pp 1–12. Published online: 12 February 2013. (DOI: 10.1017/S1479262113000014). Not open access: view abstract
Genetic variability of three cassava traits across three locations in Ghana
Peprah BB, Ofori K, Asante IK, Parkes E (2013). Genetic variability of three cassava traits across three locations in Ghana. African Journal of Plant Science 7(7):265–267 (DOI:10.5897/AJPS12.058). (G7010.01.05).
A study was conducted to assess the extent of genetic variability, broad-sense heritability and correlations for fresh root weight, root number and top weight of five cassava genotypes across three locations in 2 years. Combined analysis of variance revealed highly significant genotypic effect for all the traits. Genotype x environment interaction was also significant for all the traits studied indicating considerable but, varying response of the genotypes to the environments. High broad-sense heritability and genetic advance as percent of the mean were observed for fresh root weight, suggesting that the trait is primarily under genetic control and that a simple recurrent phenotypic selection scheme would be rewarding. Phenotypic coefficients of variation values were larger than their corresponding genotypic coefficient of variation values for all traits. Correlations between the three traits were highly significant and positive indicating that simultaneous progress for the three traits is feasible.
Peprah BB, Ofori K, Asante IK, Parkes E (2013). Genetic variability of three cassava traits across three locations in Ghana. African Journal of Plant Science 7(7):265–267 (DOI:10.5897/AJPS12.058). (G7010.01.05).
A study was conducted to assess the extent of genetic variability, broad-sense heritability and correlations for fresh root weight, root number and top weight of five cassava genotypes across three locations in 2 years. Combined analysis of variance revealed highly significant genotypic effect for all the traits. Genotype x environment interaction was also significant for all the traits studied indicating considerable but, varying response of the genotypes to the environments. High broad-sense heritability and genetic advance as percent of the mean were observed for fresh root weight, suggesting that the trait is primarily under genetic control and that a simple recurrent phenotypic selection scheme would be rewarding. Phenotypic coefficients of variation values were larger than their corresponding genotypic coefficient of variation values for all traits. Correlations between the three traits were highly significant and positive indicating that simultaneous progress for the three traits is feasible.
