Saxena RK, Edwards D and Varshney RK (2014). Structural variations in plant genomes. Briefings in Functional Genomics 13(4):296-307 (DOI: 10.1093/bfgp/elu016).

Abstract: Differences between plant genomes range from single nucleotide polymorphisms to large-scale duplications, deletions and rearrangements. The large polymorphisms are termed structural variants (SVs). SVs have received significant attention in human genetics and were found to be responsible for various chronic diseases. However, little effort has been directed towards understanding the role of SVs in plants. Many recent advances in plant genetics have resulted from improvements in high-resolution technologies for measuring SVs, including microarray-based techniques, and more recently, high-throughput DNA sequencing. In this review we describe recent reports of SV in plants and describe the genomic technologies currently used to measure these SVs.

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Bohra A, Pandey MK, Jha UC, Singh B, Singh IP, Datta D, Chaturvedi SK, Nadarajan N and Varshney RK (2014). Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects. Theoretical and Applied Genetics 127(6):1263–1291 (DOI: 10.1007/s00122-014-2301-3).

Key message: Given recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops.

Abstract: The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.

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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.

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Thudi M, Gaur PM, Krishnamurthy L, Mir RR, Kudapa H, Fikre A, Kimurto P, Tripathi S, Soren KR, Mulwa R, Bharadwaj C, Datta S, Chaturvedi SK and Varshney RK (2014). Genomics-assisted breeding for drought tolerance in chickpea. Functional Plant Biology 41(11):1178–1190 (DOI: 10.1071/FP13318).

Abstract: Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73 Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15 360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10–24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.

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Menezes CB, Carvalho Junior GA, Silva LA, Bernardino KC, Magalhães JV, Guimarães CT, Guimarães LJM and Schaffert RE (2014). Selection of sorghum hybrids grown under aluminum saturation. Genetics and Molecular Research 13(3):5964–5973 (DOI: 10.4238/2014.August.7.12).

Abstract: The purpose of this study was to evaluate 165 hybrids derived from lines previously selected for aluminum (Al) tolerance. Nine check cultivars were used, eight commercial hybrids and one experimental hybrid. Hybrids were evaluated at three levels of Al saturation (0, 20 and 40% on average). The differences between the environments were significant. Environment with 0% Al saturation yielded 29.5% more than that with 40% Al saturation, showing the importance of genotype selection for acid soils. The best check cultivar was the hybrid DKB550. The hybrids AG1020 and AG1040 also performed well, where the latter was more tolerant but the former more responsive to environment improvement. The hybrid BRS304 was susceptible to high levels of Al saturation. The three commercial BRS hybrids (BRS310, BRS330 and BRS332) performed better than BRS304 at high Al saturation. The hybrid BRS330 was the best BRS hybrid to grow on a field with high Al saturation. The hybrid DKB559 performed well at high Al saturation but did not respond to environment improvement. The hybrids 727029, 727039, 729041, 729095, 729109, AG1040, and DKB550 were tolerant to higher levels of Al saturation and responsive to environment improvement, and showed good stability and adaptability at both low and high Al saturation.

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Xangsayasane P, Jongdee B, Pantuwan G., Fukai S, Mitchell JH, Inthapanya P and Jothityangkoon D (2014). Genotypic performance under intermittent and terminal drought screening in rainfed lowland rice. Field Crops Research 156:281–292 (DOI: 10.1016/j.fcr.2013.10.017). Not open access; view abstract. (G3008.06)

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.

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)

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, Alt_SB. 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, Alt_SB, 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 Alt_SB 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 Alt_SB. 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.

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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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