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.

Leiser WL, Rattunde HFW, Weltzien E, Cisse N, Abdou M, Diallo A, Tourè AO, Magalhaes JV and Haussmann BIG (2014). Two in one sweep: aluminum tolerance and grain yield in P-limited soils are associated to the same genomic region in West African Sorghum. BMC Plant Biology 14:206 (DOI:10.1186/s12870-014-0206-6). (G7010.03.03)

Abstract: Background Sorghum (Sorghum bicolor L. Moench) productivity is severely impeded by low phosphorus (P) and aluminum (Al) toxic soils in sub-Saharan Africa and especially West Africa (WA). Improving productivity of this staple crop under these harsh conditions is crucial to improve food security and farmer’s incomes in WA.

Results This is the first study to examine the genetics underlying sorghum adaptation to phosphorus limitation in a wide range of WA growing conditions. A set of 187 diverse sorghum genotypes were grown in 29 –P and + P field experiments from 2006-2012 in three WA countries. Sorghum grain yield performance under –P and + P conditions was highly correlated (r = 0.85***). Significant genotype-by-phosphorus interaction was detected but with small magnitude compared to the genotype variance component. We observed high genetic diversity within our panel, with rapid linkage disequilibrium decay, confirming recent sequence based studies in sorghum. Using genome wide association mapping based on 220 934 SNPs we identified one genomic region on chromosome 3 that was highly associated to grain yield production. A major Al-tolerance gene in sorghum, SbMATE, was collocated in this region and SbMATE specific SNPs showed very high associations to grain yield production, especially under –P conditions, explaining up to 16% of the genotypic variance.

Conclusion The results suggest that SbMATE has a possible pleiotropic role in providing tolerance to two of the most serious abiotic stresses for sorghum in WA, Al toxicity and P deficiency. The identified SNPs can help accelerate breeding for increased sorghum productivity under unfavorable soil conditions and contribute to assuring food security in WA.

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Kijoji AA, Nchimbi-Msolla S, Kanyeka ZL, Serraj R and Henry A (2014). Linking root traits and grain yield for rainfed rice in sub-Saharan Africa: response of Oryza sativa x Oryza glaberrima introgression lines under drought. Field Crops Research 165:25–35 (DOI: 10.1016/j.fcr.2014.03.019). Not open access; view abstract. (G3008.06)

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)

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.

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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.

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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.

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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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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.

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Li X-M, He Z-H, Xiao Y-G, Xia X-C, Trethowan R, Wang H-J and Chen X-M (2014). QTL mapping for leaf senescence-related traits in common wheat under limited and full irrigation. Euphytica Published online: 2 November 2014 (DOI 10.1007/s10681-014-1272-4). Not open access; view abstract. (G7010.02.01)