Journal articles 2014
Documents
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.
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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.
Duplicate and conquer: Multiple homologs of PHOSPHORUS-STARVATION TOLERANCE1 enhance phosphorus acquisition and sorghum performance on low-phosphorus soils
Hufnagel B, de Sousa SM, Assis L, Guimaraes CT, Leiser W, Azevedo GC, Negri B, Larson BG, Shaff JE, Pastina MM, Barros BA, Weltzien E, Rattunde HFW, Viana JH, Clark RT, Falcão A, Gazaffi R, Garcia AAF, Schaffert RE, Kochian LV and Magalhaes JV (2014). Duplicate and conquer: Multiple homologs of PHOSPHORUS-STARVATION TOLERANCE1 enhance phosphorus acquisition and sorghum performance on low-phosphorus soils. Plant Physiology 166(2):659–677 (DOI:10.1104/pp.114.243949). (G7010.03.06)
Abstract: Low soil phosphorus (P) availability is a major constraint for crop production in tropical regions. The rice (Oryza sativa) protein kinase, PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was previously shown to enhance P acquisition and grain yield in rice under P deficiency. We investigated the role of homologs of OsPSTOL1 in sorghum (Sorghum bicolor) performance under low P. Association mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P conditions, in Brazil and/or in Mali. Root length and root surface area were positively correlated with grain yield under low P in the soil, emphasizing the importance of P acquisition efficiency in sorghum adaptation to low-P availability. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P in hydroponics, whereas Sb03g006765 and Sb03g0031680 alleles increasing root surface area also increased grain yield in a low-P soil. SbPSTOL1 genes colocalized with quantitative trait loci for traits underlying root morphology and dry weight accumulation under low P via linkage mapping. Consistent allelic effects for enhanced sorghum performance under low P between association panels, including enhanced grain yield under low P in the soil in Brazil, point toward a relatively stable role for Sb03g006765 across genetic backgrounds and environmental conditions. This study indicates that multiple SbPSTOL1 genes have a more general role in the root system, not only enhancing root morphology traits but also changing root system architecture, which leads to grain yield gain under low-P availability in the soil.
Hufnagel B, de Sousa SM, Assis L, Guimaraes CT, Leiser W, Azevedo GC, Negri B, Larson BG, Shaff JE, Pastina MM, Barros BA, Weltzien E, Rattunde HFW, Viana JH, Clark RT, Falcão A, Gazaffi R, Garcia AAF, Schaffert RE, Kochian LV and Magalhaes JV (2014). Duplicate and conquer: Multiple homologs of PHOSPHORUS-STARVATION TOLERANCE1 enhance phosphorus acquisition and sorghum performance on low-phosphorus soils. Plant Physiology 166(2):659–677 (DOI:10.1104/pp.114.243949). (G7010.03.06)
Abstract: Low soil phosphorus (P) availability is a major constraint for crop production in tropical regions. The rice (Oryza sativa) protein kinase, PHOSPHORUS-STARVATION TOLERANCE1 (OsPSTOL1), was previously shown to enhance P acquisition and grain yield in rice under P deficiency. We investigated the role of homologs of OsPSTOL1 in sorghum (Sorghum bicolor) performance under low P. Association mapping was undertaken in two sorghum association panels phenotyped for P uptake, root system morphology and architecture in hydroponics and grain yield and biomass accumulation under low-P conditions, in Brazil and/or in Mali. Root length and root surface area were positively correlated with grain yield under low P in the soil, emphasizing the importance of P acquisition efficiency in sorghum adaptation to low-P availability. SbPSTOL1 alleles reducing root diameter were associated with enhanced P uptake under low P in hydroponics, whereas Sb03g006765 and Sb03g0031680 alleles increasing root surface area also increased grain yield in a low-P soil. SbPSTOL1 genes colocalized with quantitative trait loci for traits underlying root morphology and dry weight accumulation under low P via linkage mapping. Consistent allelic effects for enhanced sorghum performance under low P between association panels, including enhanced grain yield under low P in the soil in Brazil, point toward a relatively stable role for Sb03g006765 across genetic backgrounds and environmental conditions. This study indicates that multiple SbPSTOL1 genes have a more general role in the root system, not only enhancing root morphology traits but also changing root system architecture, which leads to grain yield gain under low-P availability in the soil.
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)
Genetic architecture of phosphorus use efficiency in tropical maize cultivated in a low-P soil
Mendes FF, Guimarães LJM, Souza JC, Guimarães PEO, Magalhaes JV, Garcia AAF, Parentoni SN and Guimaraes CT (2014). Genetic architecture of phosphorus use efficiency in tropical maize cultivated in a low-P soil. Crop Science 54(4):1530–1538 (DOI: 10.2135/cropsci2013.11.0755). Published online 28 April 2015. (G7010.03.01)
Abstract: Phosphorus (P) deficiency is a major limiting factor for crop production in several countries. A better understanding of the genetic components of P use efficiency (PUE) is required to improve crop performance in low-P soils. To date, no QTLs (quantitative trait loci) were mapped for PUE using grain yield and other late phenotypic data in tropical conditions. Thus, we evaluated the genetic architecture of PUE in tropical maize (Zea mays L.) using multiple interval mapping for design III in a population of 140 RILs (recombinant inbred lines) backcrossed with both parental lines. The parental lines contrasted for yield and for PUE, a phenotypic index that was further decomposed into P acquisition efficiency (PAE) and P utilization efficiency. Our results showed that dominance effects were more important than additive effects for explaining the variations in PUE and its components. Approximately 80% of the QTLs mapped for PAE co-localized with those for PUE, indicating that the efficiency in acquiring P is the main determinant of PUE in tropical maize. Also, QTLs for PUE and PAE were located near to candidate genes previously associated with root development. Thus, we present important information to guide breeding strategies for the development of maize cultivars more adapted to P deficiency.
Mendes FF, Guimarães LJM, Souza JC, Guimarães PEO, Magalhaes JV, Garcia AAF, Parentoni SN and Guimaraes CT (2014). Genetic architecture of phosphorus use efficiency in tropical maize cultivated in a low-P soil. Crop Science 54(4):1530–1538 (DOI: 10.2135/cropsci2013.11.0755). Published online 28 April 2015. (G7010.03.01)
Abstract: Phosphorus (P) deficiency is a major limiting factor for crop production in several countries. A better understanding of the genetic components of P use efficiency (PUE) is required to improve crop performance in low-P soils. To date, no QTLs (quantitative trait loci) were mapped for PUE using grain yield and other late phenotypic data in tropical conditions. Thus, we evaluated the genetic architecture of PUE in tropical maize (Zea mays L.) using multiple interval mapping for design III in a population of 140 RILs (recombinant inbred lines) backcrossed with both parental lines. The parental lines contrasted for yield and for PUE, a phenotypic index that was further decomposed into P acquisition efficiency (PAE) and P utilization efficiency. Our results showed that dominance effects were more important than additive effects for explaining the variations in PUE and its components. Approximately 80% of the QTLs mapped for PAE co-localized with those for PUE, indicating that the efficiency in acquiring P is the main determinant of PUE in tropical maize. Also, QTLs for PUE and PAE were located near to candidate genes previously associated with root development. Thus, we present important information to guide breeding strategies for the development of maize cultivars more adapted to P deficiency.
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.
Root hydraulics: The forgotten side of roots in drought adaptation
Vadez V (2014). Root hydraulics: The forgotten side of roots in drought adaptation. Field Crops Research 165:15–24 (DOI: 10.1016/j.fcr.2014.03.017). (G6007.01)
Vadez V (2014). Root hydraulics: The forgotten side of roots in drought adaptation. Field Crops Research 165:15–24 (DOI: 10.1016/j.fcr.2014.03.017). (G6007.01)
Seleção de linhagens de sorgo granífero eficientes e responsivas à aplicação de fósforo (Selection of grain sorghum lines efficient and responsive to phosphorus application)
Rodrigues F, Magalhães JV, Guimarães CT, Tardin FD and Schaffert RE (2014). Seleção de linhagens de sorgo granífero eficientes e responsivas à aplicação de fósforo (Selection of grain sorghum lines efficient and responsive to phosphorus application). Pesquisa Agropecuária Brasileira 49(8):613–621 (DOI: 10.1590/S0100-204X2014000800005). Article in Portuguese with abstract in English. (G7010.03.06)
Abstract: The objective of this work was to select sorghum lines simultaneously responsive to phosphorus fertilization and with high productive efficiency regarding this nutrient. Thirty six sorghum inbred lines were evaluated in a randomized complete block design, with two replicates. The traits used to evaluate the productive efficiency were average yield and efficiencies of absorption, utilization, and use of phosphorus, with and without phosphorus fertilization. For the analysis of the responsivity to the nutrient, the evaluated traits were relative yield and apparent recovery, physiological, and agronomic efficiencies. The lines were genetically divergent as to the efficiencies of absorption, utilization, and use of phosphorus, and to the responsivity to the nutrient, suggesting the possibility of producing hybrids destined to different market niches. The most responsive lines were P9401, BR007B, BR008B, SC414-12E, and SC566, and the most efficient ones under low phosphorus availability were ATF40B, SC566, BR005R, CMSXS225, and BR012 (R6). The ATF40B, ATF54 (f61), ATF54 (f596), QL3, and SC566 lines showed better simultaneous performance for the different evaluated efficiencies and for the responsivity to phosphorus. The evaluation of productivity alone, under different phosphorus availabilities, already makes it possible to identify efficient and responsive lines to phosphorus.
Rodrigues F, Magalhães JV, Guimarães CT, Tardin FD and Schaffert RE (2014). Seleção de linhagens de sorgo granífero eficientes e responsivas à aplicação de fósforo (Selection of grain sorghum lines efficient and responsive to phosphorus application). Pesquisa Agropecuária Brasileira 49(8):613–621 (DOI: 10.1590/S0100-204X2014000800005). Article in Portuguese with abstract in English. (G7010.03.06)
Abstract: The objective of this work was to select sorghum lines simultaneously responsive to phosphorus fertilization and with high productive efficiency regarding this nutrient. Thirty six sorghum inbred lines were evaluated in a randomized complete block design, with two replicates. The traits used to evaluate the productive efficiency were average yield and efficiencies of absorption, utilization, and use of phosphorus, with and without phosphorus fertilization. For the analysis of the responsivity to the nutrient, the evaluated traits were relative yield and apparent recovery, physiological, and agronomic efficiencies. The lines were genetically divergent as to the efficiencies of absorption, utilization, and use of phosphorus, and to the responsivity to the nutrient, suggesting the possibility of producing hybrids destined to different market niches. The most responsive lines were P9401, BR007B, BR008B, SC414-12E, and SC566, and the most efficient ones under low phosphorus availability were ATF40B, SC566, BR005R, CMSXS225, and BR012 (R6). The ATF40B, ATF54 (f61), ATF54 (f596), QL3, and SC566 lines showed better simultaneous performance for the different evaluated efficiencies and for the responsivity to phosphorus. The evaluation of productivity alone, under different phosphorus availabilities, already makes it possible to identify efficient and responsive lines to phosphorus.
Genomewide association studies for 50 agronomic traits in peanut using the ‘reference set’ comprising 300 genotypes from 48 countries of the semi-arid tropics of the world
Pandey MK, Upadhyaya HD, Rathore A, Vadez V, Sheshshayee MS, Sriswathi M, Govil M, Kumar A, Gowda MVC, Sharma S, Hamidou F, Kumar VA, Khera P, Bhat RS, Khan AW, Singh S, Li H, Monyo E, Nadaf HL, Mukri G, Jackson SA, Guo B, Liang X and Varshney RK (2014). Genomewide association studies for 50 agronomic traits in peanut using the ‘reference set’ comprising 300 genotypes from 48 countries of the semi-arid tropics of the world. PLoS ONE 9(8):e105228 (DOI:10.1371/journal.pone.0105228).
Abstract: Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the ‘reference set’ of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15–20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (pvalue .2.1610–6) with wide phenotypic variance (PV) range (5.81–90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.
Pandey MK, Upadhyaya HD, Rathore A, Vadez V, Sheshshayee MS, Sriswathi M, Govil M, Kumar A, Gowda MVC, Sharma S, Hamidou F, Kumar VA, Khera P, Bhat RS, Khan AW, Singh S, Li H, Monyo E, Nadaf HL, Mukri G, Jackson SA, Guo B, Liang X and Varshney RK (2014). Genomewide association studies for 50 agronomic traits in peanut using the ‘reference set’ comprising 300 genotypes from 48 countries of the semi-arid tropics of the world. PLoS ONE 9(8):e105228 (DOI:10.1371/journal.pone.0105228).
Abstract: Peanut is an important and nutritious agricultural commodity and a livelihood of many small-holder farmers in the semi-arid tropics (SAT) of world which are facing serious production threats. Integration of genomics tools with on-going genetic improvement approaches is expected to facilitate accelerated development of improved cultivars. Therefore, high-resolution genotyping and multiple season phenotyping data for 50 important agronomic, disease and quality traits were generated on the ‘reference set’ of peanut. This study reports comprehensive analyses of allelic diversity, population structure, linkage disequilibrium (LD) decay and marker-trait association (MTA) in peanut. Distinctness of all the genotypes can be established by using either an unique allele detected by a single SSR or a combination of unique alleles by two or more than two SSR markers. As expected, DArT features (2.0 alleles/locus, 0.125 PIC) showed lower allele frequency and polymorphic information content (PIC) than SSRs (22.21 alleles /locus, 0.715 PIC). Both marker types clearly differentiated the genotypes of diploids from tetraploids. Multi-allelic SSRs identified three sub-groups (K = 3) while the LD simulation trend line based on squared-allele frequency correlations (r2) predicted LD decay of 15–20 cM in peanut genome. Detailed analysis identified a total of 524 highly significant MTAs (pvalue .2.1610–6) with wide phenotypic variance (PV) range (5.81–90.09%) for 36 traits. These MTAs after validation may be deployed in improving biotic resistance, oil/ seed/ nutritional quality, drought tolerance related traits, and yield/ yield components.
Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches
Thudi M, Upadhyaya HD, Rathore A, Gaur PM, Krishnamurthy L, Roorkiwal M, Nayak SN, Chaturvedi SK, Basu PS, Gangarao NVPR, Fikre A, Kimurto P, Sharma PC, Sheshashayee MS, Tobita S, Kashiwagi J, Ito O, Killian A and Varshney RK (2014). Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches. PLoS ONE 9(5):e96758 (DOI: 10.1371/journal.pone.0096758).
Abstract: To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1–7 seasons and 1–3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1 SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.
Thudi M, Upadhyaya HD, Rathore A, Gaur PM, Krishnamurthy L, Roorkiwal M, Nayak SN, Chaturvedi SK, Basu PS, Gangarao NVPR, Fikre A, Kimurto P, Sharma PC, Sheshashayee MS, Tobita S, Kashiwagi J, Ito O, Killian A and Varshney RK (2014). Genetic dissection of drought and heat tolerance in chickpea through genome-wide and candidate gene-based association mapping approaches. PLoS ONE 9(5):e96758 (DOI: 10.1371/journal.pone.0096758).
Abstract: To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1–7 seasons and 1–3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1 SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.
