Varshney RK, Mir RR, Bhatia S, Thudi M, Hu Y, Azam S, Zhang Y, Jaganathan D, You FM, Gao J, Riera-Lizarazu O and Luo MC (2014). Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Functional & Integrative Genomics 14(1): 59–73 (DOI: 10.1007/s10142-014-0363-6).

Abstract: Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.

 Full article

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)

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.

 Full article

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.

 Full article

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.

 Full article

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)

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.

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.

 Full article

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.

 Full article

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)