Insights into genetic diversity and population structure of Indian carrot (Daucus carota L.) accessions.

Carrot (Daucus carota L.) is acknowledged as a highly valuable vegetable crop. Despite having high demand, limited breeding efforts have been made to develop the varieties and hybrids suitable to wider climatic conditions due to improper characterization of the available germplasm. An accession panel (AP) consisting of 144 accessions of five different root colors representing Asiatic and Western gene pools collected from different parts of India was utilized in the present study. This diverse AP was used to assess the population structure and genetic diversity from 80 polymorphic DNA markers distributed throughout the genome. Population structure, neighbor-joining (NJ) tree, and principal coordinate analysis (PCoA)-based diversity assessment divided the AP into three subpopulations/clusters. Greater than ninety percent polymorphism and the higher average polymorphic information content (͂> 0.50) coupled with higher gene diversity (He) indicating the broad genetic base of the population. Moderate to high Fst and gene flow (Nm) between the subpopulations revealed a moderate genetic differentiation among Indian carrot accessions owing to the highly outcrossing nature of carrot. Analysis of molecular variance (AMOVA) exhibited higher variation among individuals within the subpopulations (69.00%) or total populations (19.00%) than among the subpopulations (13%) as expected in the single Daucus species used here. The information obtained in the study would benefit the carrot breeders to explore the genetic diversity of the Indian carrots in the carrot breeding program for widening the genetic base and multi-color target trait improvement.

Identification of Coupling and Repulsion Phase DNA Marker Associated With an Allele of a Gene Conferring Host Plant Resistance to Pigeonpea sterility mosaic virus (PPSMV) in Pigeonpea (Cajanus cajan L. Millsp.).

Pigeonpea Sterility Mosaic Disease (PSMD) is an important foliar disease caused by Pigeonpea sterility mosaic virus (PPSMV) which is transmitted by eriophyid mites (Aceria cajani Channabasavanna). In present study, a F2 mapping population comprising 325 individuals was developed by crossing PSMD susceptible genotype (Gullyal white) and PSMD resistant genotype (BSMR 736). We identified a set of 32 out of 300 short decamer random DNA markers that showed polymorphism between Gullyal white and BSMR 736 parents. Among them, eleven DNA markers showed polymorphism including coupling and repulsion phase type of polymorphism across the parents. Bulked Segregant Analysis (BSA), revealed that the DNA marker, IABTPPN7, produced a single coupling phase marker (IABTPPN7414) and a repulsion phase marker (IABTPPN7983) co-segregating with PSMD reaction. Screening of 325 F2 population using IABTPPN7 revealed that the repulsion phase marker, IABTPPN7983, was co-segregating with the PSMD responsive SV1 at a distance of 23.9 cM for Bidar PPSMV isolate. On the other hand, the coupling phase marker IABTPPN7414 did not show any linkage with PSMD resistance. Additionally, single marker analysis both IABTPPN7983 (P<0.0001) and IABTPPN 7414 (P<0.0001) recorded a significant association with the PSMD resistance and explained a phenotypic variance of 31 and 36% respectively in F2 population. The repulsion phase marker, IABTPPN7983, could be of use in Marker-Assisted Selection (MAS) in the PPSMV resistance breeding programmes of pigeonpea.

Inheritance of pigeonpea sterility mosaic disease resistance in pigeonpea.

A comprehensive study was conducted using PPSMV resistant (BSMR 736) and susceptible (ICP 8863) genotypes to develop a segregating population and understand the inheritance of PPSMV resistance. The observed segregation was comparable to 13 (susceptible): 3 (resistant). Hence, the inheritance was controlled by two genes, SV1 and SV2, with inhibitory gene interaction.

Molecular mapping of genomic regions harbouring QTLs for root and yield traits in sorghum (Sorghum bicolor L. Moench).

Root system is a vital part of plants for absorbing soil moisture and nutrients and it influences the drought tolerance. Identification of the genomic regions harbouring quantitative trait loci (QTLs) for root and yield traits, and the linked markers can facilitate sorghum improvement through marker-assisted selection (MAS) besides the deeper understanding of the plant response to drought stress. A population of 184 recombinant inbred lines (RILs), derived from E36-1 × SPV570, along with parents were phenotyped for component traits of yield in field and root traits in an above ground rhizotron. High estimates of heritability and genetic advance for all the root traits and for most of the yield traits, presents high scope for improvement of these traits by simple selection. A linkage map constructed with 104 marker loci comprising 50 EST-SSRs, 34 non-genic nuclear SSRs and 20 SNPs, and QTL analysis was performed using composite interval mapping (CIM) approach. A total of eight and 20 QTLs were mapped for root and yield related traits respectively. The QTLs for root volume, root fresh weight and root dry weight were found co-localized on SBI-04, supported by a positive correlation among these traits. Hence, these traits can be improved using the same linked markers. The lack of overlap between the QTLs of component traits of root and yield suggested that these two sets of parameters are independent in their influence and the possibility of combining these two traits might enhance productivity of sorghum under receding moisture condition.

Quantitative RT-PCR analysis of 20 transcription factor genes of MADS, ARF, HAP2, MBF and HB families in moisture stressed shoot and root tissues of sorghum.

Transcription factors (TFs) are an important target in understanding the regulation of plant responses to environmental stress including moisture stress. Members of the same TF family may differ in their response to moisture stress. The expression pattern could vary between shoot and root tissues depending on level of moisture stress. A set of five rarely studied TF families viz., MADS-box (MCM1, AGAMOUS, DEFICIENS and SRF), Auxin Responsive Factor (ARF), Heme Activator Protein 2 (HAP2), Multiprotein Bridging Factor (MBF) and Homeobox (HB) together having 20 members in sorghum, were expression analyzed through quantitative real-time PCR (qRT-PCR) in well watered and moisture stressed shoot and root tissues of sorghum using SYBR Green® to quantify dsDNA synthesis. Fluorescence values were used to calculate PCR efficiency by using LinRegPCR. The PTSb00029.1 and PTSb00033.1 of ARF family and PTSb00174.1 and PTSb00175.1 of HB family recorded 2 to 5, PTSb00221.1 and PTSb00208.1 of MADS family and PTSb00128.1 of HAP2 family recorded 5 to 10 fold up-regulation under moisture stress regimes. The PTSb00128.1, a HAP2 family member, recorded 15 fold up-regulation in mild moisture stressed root tissues. TF genes such as PTSb00218.1, PTSb00220.1, PTSb00031.1, PTSb00032.1, PTSb00034.1 and PTSb00223.1 were found down regulating in both tissues types under moisture stress condition. However, the PTSb00128.1, PTSb00221.1, PTSb00029.1, PTSb00033.1 and PTSb00174.1 TFs were found up-regulating to varied levels in mild and severe moisture stressed root tissues only. Verification of qRT-PCR results was done by in situ hybridization (ISH) of randomly selected two TF genes in shoot and root tissues of sorghum. Taken together, moisture stress triggered up-regulation of more genes in root tissue compared to shoot tissue in sorghum.

Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.).

Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an 'orphan crop legume'. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation's Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an 'orphan legume crop' to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.

RAPD cluster analysis and chlorate sensitivity of some Indian isolates of Macrophomina phaseolina from sorghum and their relationships with pathogenicity.

Charcoal rot caused by Macrophomina phaseolina is an economically important disease in sorghum grown during the post rainy season in India. Variations in random amplified polymorphic DNA (RAPD) polymorphisms, chlorate sensitivity and pathogenicity were studied among sorghum isolates of M. phaseolina collected from different parts of India. RAPD data based on 14 random primers of Kit A and C (OPA and OPC) on 20 isolates showed a high degree of polymorphism (98.1%) in different isolates. UPGMA dendrogram on RAPD data produced 7 clusters at the level of 37% similarity. Isolates from the same locations showed a tendency to group closer, substantiating closer genetic relatedness. Sorghum infecting Macrophomina isolates showed a mixed response for sensitivity to potassium chlorate (120 mM). Chlorate-resistant isolates were predominant (>65% of the isolates) over sensitive isolates. Chlorate-sensitive isolates were found to be genetically closer among them than the resistant ones. For the first time it was shown that chlorate sensitivity in Macrophomina had some relations with charcoal rot severity in sorghum.