Study of interspecific SSR polymorphism among 14 species from Triticum-Aegilops group

In the present study, using in-gel hybridization and PCR based approaches, interspecific SSR polymorphism was studied among 14 species of Triticum-Aegilops group. The material represented seven different genomes and three ploidy levels (2x,4x,6x). In-gel hybridization involved 13 probe-enzyme combinations (four SSR oligonucleotide probes in combination with 2-4 enzymes) and resolved 5 to 20 bands (0.40kb to > 23kb) in each of the 14 individual species. This suggested ubiquitous distribution and interspecific polymorphism of SSRs among different species of Triticum-Aegilops group. The available polymorphism also proved helpful in discriminating not only the species with different ploidy levels and possessing different genomes, but also those possessing similar or very closely related genomes. The amplification of SSR loci using 15 primer pairs derived from hexaploid wheat was also carried out in all the 14 species. The primer pairs, each amplified SSR loci not only in species containing A, B and D genomes, but also in 2 to 10 of the remaining species that contained other genomes. This suggested that wheat SSRS might have been derived from the corresponding SSRs in an ancestral genome and are conserved across a number of species in the Triticum-Aegilops group. Also, two pairs of SSRs (one consisting of WMC243 and WMC415 and the other consisting of WMC35 and WMC404) each discriminated all the 14 species examined during the present study. Therefore, one can infer from the present study that SSR primers can be used in studies on DNA polymorphism, genetic diversity, gene mapping and synteny conservation across different species of Triticum-Aegilops group

Marker‐Assisted Backcrossing to Introgress Resistance to Fusarium Wilt Race 1 and Ascochyta Blight in C 214, an Elite Cultivar of Chickpea

Fusarium wilt (FW) and Ascochyta blight (AB) are two major constraints to chickpea (Cicer arietinum L.) production. Therefore, two parallel marker-assisted backcrossing (MABC) programs by targeting foc1 locus and two quantitative trait loci (QTL) regions, ABQTL-I and ABQTL-II, were undertaken to introgress resistance to FW and AB, respectively, in C 214, an elite cultivar of chickpea. In the case of FW, foreground selection (FGS) was conducted with six markers (TR19, TA194, TAA60, GA16, TA110, and TS82) linked to foc1 in the cross C 214 × WR 315 (FW-resistant). On the other hand, eight markers (TA194, TR58, TS82, GA16, SCY17, TA130, TA2, and GAA47) linked with ABQTL-I and ABQTL-II were used in the case of AB by deploying C 214 × ILC 3279 (AB-resistant) cross. Background selection (BGS) in both crosses was employed with evenly distributed 40 (C 214 × WR 315) to 43 (C 214 × ILC 3279) SSR markers in the chickpea genome to select plant(s) with higher recurrent parent genome (RPG) recovery. By using three backcrosses and three rounds of selfing, 22 BC3F4 lines were generated for C 214 × WR 315 cross and 14 MABC lines for C 214 × ILC 3279 cross. Phenotyping of these lines has identified three resistant lines (with 92.7–95.2% RPG) to race 1 of FW, and seven resistant lines (with 81.7–85.40% RPG) to AB that may be tested for yield and other agronomic traits under multilocation trials for possible release and cultivation

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]

<p>Abstract</p> <p>Background</p> <p>Pigeonpea [<it>Cajanus cajan </it>(L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping.</p> <p>Results</p> <p>In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped <it>in silico </it>identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population.</p> <p>Conclusion</p> <p>We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus <it>Cajanus</it>. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.</p

Construction of a high-density genetic map and QTL analysis for yield, yield components and agronomic traits in chickpea (Cicer arietinum L.)

Unravelling the genetic architecture underlying yield components and agronomic traits is important for enhancing crop productivity. Here, a recombinant inbred line (RIL) population, developed from ICC 4958 and DCP 92–3 cross, was used for constructing linkage map and QTL mapping analysis. The RIL population was genotyped using a high-throughput Axiom®- CicerSNP array, which enabled the development of a high-density genetic map consisting of 3,818 SNP markers and spanning a distance of 1064.14 cM. Analysis of phenotyping data for yield, yield components and agronomic traits measured across three years together with genetic mapping data led to the identification of 10 major-effect QTLs and six minoreffect QTLs explaining up to 59.70% phenotypic variance. The major-effect QTLs identified for 100-seed weight, and plant height possessed key genes, such as C3HC4 RING finger protein, pentatricopeptide repeat (PPR) protein, sugar transporter, leucine zipper protein and NADH dehydrogenase, amongst others. The gene ontology studies highlighted the role of these genes in regulating seed weight and plant height in crop plants. The identified genomic regions for yield, yield components, and agronomic traits, and the closely linked markers will help advance genetics research and breeding programs in chickpea

A FRUITFULL-like gene is associated with genetic variation for fruit flesh firmness in apple (Malus domestica Borkh.)

The FRUITFULL (FUL) and SHATTERPROOF (SHP) genes are involved in regulating fruit development and dehiscence in Arabidopsis. We tested the hypothesis that this class of genes are also involved in regulating the development of fleshy fruits, by exploring genetic and phenotypic variation within the apple (Malus domestica) gene pool. We isolated and characterised the genomic sequences of two candidate orthologous FUL-like genes, MdMADS2.1 and MdMADS2.2. These were mapped using the reference population ‘Prima x Fiesta’ to loci on Malus linkage groups LG14 and LG06, respectively. An additional MADS-box gene, MdMADS14, shares high amino acid identity with the Arabidopsis SHATTERPROOF1/2 genes and was mapped to Malus linkage group LG09. Association analysis between quantitative fruit flesh firmness estimates of ‘Prima x Fiesta’ progeny and the MdMADS2.1, MdMADS2.2 and MdMADS14 loci was carried out using a mixed model analysis of variance. This revealed a significant association (P < 0.01) between MdMADS2.1 and fruit flesh firmness. Further evidence for the association between MdMADS2.1 and fruit flesh firmness was obtained using a case–control population-based genetic association approach. For this, a polymorphic repeat, (AT)n, in the 3′ UTR of MdMADS2.1 was used as a locus-specific marker to screen 168 apple accessions for which historical assessments of fruit texture attributes were available. This analysis revealed a significant association between the MdMADS2.1 and fruit flesh firmness at both allelic (χ 2 = 34, df = 9, P < 0.001) and genotypic (χ 2 = 57, df = 32, P < 0.01) levels

Genomics interventions in crop breeding for sustainable agriculture

There has been significant improvement in production and productivity of important cereal crops globally as a consequence of the “Green Revolution” and other initiatives (1). However, today the stage has reached that the available traditional methods of crop improvement are not sufficient to provide enough and staple food grains to the constantly growing world population (2). This situation is projected to be worse by the year 2050 especially in context of climate change (3). In other words, the conventional plant breeding practices may not able to achieve the sustainability in today’s agriculture...

Genomics interventions in crop breeding for sustainable agriculture

There has been significant improvement in production and productivity of important cereal crops globally as a consequence of the “Green Revolution” and other initiatives (1). However, today the stage has reached that the available traditional methods of crop improvement are not sufficient to provide enough and staple food grains to the constantly growing world population (2). This situation is projected to be worse by the year 2050 especially in context of climate change (3). In other words, the conventional plant breeding practices may not able to achieve the sustainability in today’s agriculture...

Integrated Wasteland Development Project (IWDP-Batch I) Medak District Andhra Pradesh

Farmers in different villages confirmed that water level in open wells increased on an average in the range of 3 to 15 feet during the SW monsoon rainy season and availability is extended by about 2 months in the dry season during year. Farmers mentioned that period of water availability in open wells for irrigation extended from January before the IWDP initiative to end of March after the watershed development. This situation favored a change to double cropping with four or six supplemental irrigations for second crop between January to March. All this impact was felt by the beneficiaries because of good quality soil and water conservation interventions and water harvesting structures at right location developed through this project. Commendable efforts by the project managers, staff, as well as WC were responsible for these positive impacts in these watersheds