Molecular markers for late blight resistance breeding of potato: an update

Late blight is the most devastating disease of the potato crop that can be effectively managed by growing resistant cultivars. Introgression of resistance (R) genes/quantitative trait loci (QTLs) from the Solanum germplasm into common potato is one of the plausible approaches to breed resistant cultivars. Although the conventional method of breeding will continue to play a primary role in potato improvement, molecular marker technology is becoming one of its integral components. To achieve rapid success, from the past to recent years, several R genes/QTLs that originated from wild/cultivated Solanum species were mapped on the potato genome and a few genes were cloned using molecular approaches. As a result, molecular markers closely linked to resistance genes or QTLs offer a quicker potato breeding option through marker‐assisted selection (MAS). However, limited progress has been achieved so far through MAS in potato breeding. In near future, new resistance genes/QTLs are expected to be discovered from wild Solanum gene pools and linked molecular markers would be available for MAS. This article presents an update on the development of molecular markers linked to late blight resistance genes or QTLs by utilization of Solanum species for MAS in potato.     

Regeneration of tree species in the sub-tropical forest of Alaknanda Valley, Garhwal Himalaya, India

We studied the regeneration of tree species in the sub-tropical forest of Alaknanda Valley in Garhwal Himalaya, India. The overall regeneration status was fairly good in the study area. Seedling density ranged between 520 and 1,240 seedlings per ha while the density of saplings varied between 400 and 800 saplings per ha. Out of eight sites studied, five sites, viz., A1 , A2 , B1 , B2and C2contained the highest number of seedlings (280-480 per ha) and saplings (200-440 per ha) for Pinus roxburghii and remaining three sites viz., C1, D1and D2represented the highest number of seedlings (240-400 per ha) and saplings (200-240 per ha) for Anogeissus latifolius. The DBH class distribution of the tree species revealed that the highest number of individuals was concentrated in the lower diameter classes while smallest numbers were found in the higher diameter classes. Species such as Acacia catechu, Anogeissus latifolius, Dalbergia sissoo, Engelhardtia spicata, Lannea coromandelica, Mallotus philippensis and Pinus roxburghii have the largest number of saplings and seedlings in the lower DBH classes, suggesting that they have good regeneration potential. Other species such as Aegle marmelos, Bauhinia variegata, Bombax ceiba, Cassia fistula, Erythrina variegata, Haldinia cordifolia, Mangifera indica, Ougeinia oojeinensis, Phyllanthus emblica, Syzygium cumini, Terminalia alata and Toona hexandra have either no or very small number of saplings in the lower DBH classes, which indicates that the status of these species implies poor regeneration.     

Identification of bovine viral diarrhea virus type 1 in yaks (Bos poephagus grunniens) in the Himalayan region

Since cattle are widely infected by bovine viral diarrhea virus (BVDV) in India, we searched for pestivirus infection in yaks. Of 71 pure and crossbred yaks from Himalayan region, pestivirus antigen was detected by Ag-ELISA in three animals. Pestivirus in leukocyte and cell culture isolated virus samples originating from positive yaks was also confirmed by RT-PCR using panpestivirus specific primers selected from 5'-untranslated region (5' UTR). The 5' UTR, N(pro) and E2 regions were sequenced and used for genetic typing. Phylogenetic analysis revealed that pestiviruses detected in three Himalayan yaks were similar genetically, belonging to BVDV-1. Antigenic characterisation of yak pestivirus also confirmed the typing as BVDV-1. This is the first report on the identification of BVDV type 1 in yaks.     

Development and evaluation of a high-throughput,low-cost genotyping platform based on oligonucleotide microarrays in rice

Background  

We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features.     

Se18.9, an anti-phagocytic factor H binding protein of Streptococcus equi

Evasion of phagocytosis is an important virulence determinant of Streptococcus equi (S. equi subsp. equi), the cause of equine strangles and distinguishes it from the closely related but much less virulent S. zooepidemicus (S. equi subsp. zooepidemicus). We describe Se18.9, a novel H factor binding protein secreted by S. equi but not by S. zooepidemicus that reduces deposition of C3 on the bacterial surface and significantly reduces the bactericidal activity of equine neutrophils suspended in normal serum for both S. equi and S. zooepidemicus. Se18.9 is secreted abundantly by actively dividing cells and is also bound to the bacterial surface. Strong serum and mucosal antibody responses are elicited in S. equi infected horses. Although a gene identical to se18.9 was not detected in S. zooepidemicus, sequences encoding proteins of similar size with similar signal peptide sequences were found in 3 of 12 randomly selected strains. Since Se18.9 is unique to S. equi, and immunoreactive with convalescent sera and mucosal IgA, it has potential for immunodiagnosis and for study of mucosal antibody response to S. equi.     

Development of simplified and rapid nucleic acid release protocol for PCR based detection of <Emphasis Type="Italic">Potato viruses</Emphasis>

A simple, cost-effective and rapid viral nucleic acid release (NAR) buffer suitable for RT-PCR based diagnostic assay was developed for the detection of potato viruses. The NAR buffer and commercially available RNA isolation kit were compared for RT-PCR based assay, where an amplicon of expected size (~380 bp) targeting PVY was observed in both isolations indicating that it can be used in RT-PCR based diagnostic assays. The same was further validated for its repeatability by running across more than hundred suspected potato leaf samples collected from different sources where, it showed consistent results for the presence of PVY indicating its reliability. The NAR buffer assay was examined for its sensitivity in comparison with the kit based isolation where both the assays were able to detect even up to 10^?5 dilution without affecting the sensitivity. NAR buffer was found stable up to 28 days at -20 °C and for 14 days at 4 °C without losing PCR sensitivity. The assay was also found effective to release the nucleic acid from potato leaves, thrips and aphids for PCR and RT-PCR based detection of DNA viruses like ToLCNDV-potato and other RNA viruses. The developed protocol is simple, less laborious, time-saving (10-15 min) and economical (1/100th of kit) as compared to kit based protocol. The assay can be adopted in diagnostic laboratories for detection of RNA/DNA viruses from potato plants and in thrips as well.     

Evaluation and utilization of <Emphasis Type="Italic">Aegilops</Emphasis> and wild <Emphasis Type="Italic">Triticum</Emphasis> species for enhancing iron and zinc content in wheat

Grains of 80 accessions of nine species of wild Triticum and Aegilops along with 15 semi-dwarf cultivars of bread and durum wheat grown over 2 years at Indian Institute of Technology, Roorkee, were analyzed for grain iron and zinc content. The bread and durum cultivars had very low content and little variability for both of these micronutrients. The related non-progenitor wild species with S, U and M genomes showed up to 3–4 folds higher iron and zinc content in their grains as compared to bread and durum wheat. For confirmation, two Ae. kotschyi Boiss. accessions were analyzed after ashing and were found to have more than 30% higher grain ash content than the wheat cultivars containing more than 75% higher iron and 60% higher zinc than that of wheat. There were highly significant differences for iron and zinc contents among various cultivars and wild relatives over both the years with very high broad sense heritability. There was a significantly high positive correlation between flag leaf iron and grain iron (r = 0.82) and flag leaf zinc and grain zinc (r = 0.92) content of the selected donors suggesting that the leaf analysis could be used for early selection for high iron and zinc content. ‘Chinese Spring’ (Ph ^I ) was used for inducing homoeologous chromosome pairing between Aegilops and wheat genomes and transferring these useful traits from the wild species to the elite wheat cultivars. A majority of the interspecific hybrids had higher leaf iron and zinc content than their wheat parents and equivalent or higher content than their Aegilops parents suggesting that the parental Aegilops donors possess a more efficient system for uptake and translocation of the micronutrients which could ultimately be utilized for wheat grain biofortification. Partially fertile to sterile BC₁ derivatives with variable chromosomes of Aegilops species had also higher leaf iron and zinc content confirming the possibility of transfer of required variability. Some of the fertile BC₁F₃ and BC₂F₂ derivatives had as high grain ash and grain ash iron and zinc content as that of the donor Aegilops parent. Further work on backcrossing, selfing, selection of fertile derivatives, leaf and grain analyses for iron and zinc for developing biofortified bread and durum wheat cultivars is in progress. Nidhi Rawat, Vijay K. Tiwari, and Neelam Singh have contributed equally to the work.