Varshney RK, Pandey MK, Pasupuleti J, Nigam SN, Sudini H, Gowda MVC, Sriswathi M, Radhakrishnan T, Manohar SS and Nagesh P (2014). Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theoretical and Applied Genetics. Published online: 14 June 2014 (DOI: 10.1007/s00122-014-2338-3).

Key message: Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield.

Abstract: Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.

 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)

Azam S, Rathore A, Shah TM, Telluri M, Amindala B, Ruperao P, Katta MAVS and Varshney RK (2014). An Integrated SNP Mining and Utilization (ISMU) pipeline for next generation sequencing data. PLoS ONE 9(7):e101754 (DOI:10.1371/journal.pone.0101754).

Abstract: Open source single nucleotide polymorphism (SNP) discovery pipelines for next generation sequencing data commonly requires working knowledge of command line interface, massive computational resources and expertise which is a daunting task for biologists. Further, the SNP information generated may not be readily used for downstream processes such as genotyping. Hence, a comprehensive pipeline has been developed by integrating several open source next generation sequencing (NGS) tools along with a graphical user interface called Integrated SNP Mining and Utilization (ISMU) for SNP discovery and their utilization by developing genotyping assays. The pipeline features functionalities such as pre-processing of raw data, integration of open source alignment tools (Bowtie2, BWA, Maq, NovoAlign and SOAP2), SNP prediction (SAMtools/SOAPsnp/CNS2snp and CbCC) methods and interfaces for developing genotyping assays. The pipeline outputs a list of high quality SNPs between all pairwise combinations of genotypes analyzed, in addition to the reference genome/sequence. Visualization tools (Tablet and Flapjack) integrated into the pipeline enable inspection of the alignment and errors, if any. The pipeline also provides a confidence score or polymorphism information content value with flanking sequences for identified SNPs in standard format required for developing marker genotyping (KASP and Golden Gate) assays. The pipeline enables users to process a range of NGS datasets such as whole genome re-sequencing, restriction site associated DNA sequencing and transcriptome sequencing data at a fast speed. The pipeline is very useful for plant genetics and breeding community with no computational expertise in order to discover SNPs and utilize in genomics, genetics and breeding studies. The pipeline has been parallelized to process huge datasets of next generation sequencing. It has been developed in Java language and is available at http://hpc.icrisat.cgiar.org/ISMU as a standalone free software.

 Full article

Roorkiwal M, von Wettberg EJ, Upadhyaya HD, Warschefsky E, Rathore A and Varshney RK (2014). Exploring germplasm diversity to understand the domestication process in Cicer spp. using SNP and DArT markers. PLoS ONE 9(7):e102016 (DOI: 10.1371/journal.pone.0102016).

Abstract: To estimate genetic diversity within and between 10 interfertile Cicer species (94 genotypes) from the primary, secondary and tertiary gene pool, we analysed 5,257 DArT markers and 651 KASPar SNP markers. Based on successful allele calling in the tertiary gene pool, 2,763 DArT and 624 SNP markers that are polymorphic between genotypes from the gene pools were analyzed further. STRUCTURE analyses were consistent with 3 cultivated populations, representing kabuli, desi and pea-shaped seed types, with substantial admixture among these groups, while two wild populations were observed using DArT markers. AMOVA was used to partition variance among hierarchical sets of landraces and wild species at both the geographical and species level, with 61% of the variation found between species, and 39% within species. Molecular variance among the wild species was high (39%) compared to the variation present in cultivated material (10%). Observed heterozygosity was higher in wild species than the cultivated species for each linkage group. Our results support the Fertile Crescent both as the center of domestication and diversification of chickpea. The collection used in the present study covers all the three regions of historical chickpea cultivation, with the highest diversity in the Fertile Crescent region. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa in the past.

 Full article

Al-Shugeairy Z, Islam MS, Shrestha R, Al-Ogaidi F, Norton GJ and Price AH (2014). High throughput screening of rooting depth in rice using buried herbicide. Annals of Applied Biology 165(1):96–107 (DOI: 10.1111/aab.12118). 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.

Li X-M, Chen X-M, Xiao Y-G, Xia X-C, Wang D-S, He Z-H and Wang H-J (2014). Identification of QTLs for seedling vigor in winter wheat. Euphytica 198(2):199–209 (DOI: 10.1007/s10681-014-1092-6). Not open access; view abstract. (G7010.02.01)

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.

 Full article

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.

 Full article

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.

 Full article