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Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment. [ABSTRACT FROM AUTHOR]

Summary: We had the fortune of starting our scientific/research careers in the Molecular Biology and Crop Biotechnology Laboratory of Professor P.K. Gupta at Ch. Charan Singh University, Meerut, UP, India. Here, we describe the most important scientific contributions of our beloved mentor in the area of cytotaxonomy, cytogenetics, mutation breeding, quantitative genetics, molecular biology, crop biotechnology and plant genomics, on his 85th birthday. Important contributions made in the development and use of genomics resources including the development and use of different kinds of molecular markers, genetic and physical mapping, quantitative trait locus (QTL) interval mapping, genome‐wide association mapping and molecular breeding including marker‐assisted selection have been briefly summarized. Efforts have been also made to give readers a glimpse of important contributions in the study of cytology/apomixis of grasses, cytotaxonomic studies in asteraceae/fabaceae, nuclear/repetitive DNA content in Lolium, interspecific/intergeneric relationships involving the genus Hordeum and re‐examining taxonomy of the tribe Triticeae. [ABSTRACT FROM AUTHOR]

Black pepper is one of the most valued and widely used spices in the world and dominates multi-billion dollar global spices trade. India is amongst the major producers, consumers and exporters of black pepper. In spite of its commercial and cultural importance, black pepper has received meagre attention in terms of generation of genomic resources. Availability of markers distributed throughout the genome would facilitate and accelerate genetic studies, QTL identification, genetic enhancement and crop improvement in black pepper. In this perspective, the sequence information from the recently sequenced black pepper (Piper nigrum) genome has been used for identification and characterisation of Simple Sequence Repeats (SSRs). Total 69,126 SSRs were identified from assembled genomic sequence of P. nigrum. The SSR frequency was 158 per MB making it, one SSR for every 6.3 kb in the assembled genome. Among the different types of microsatellite repeat motifs, dinucleotides were the most abundant (48.6%), followed by trinucleotide (23.7%) and compound repeats (20.62%). A set of 85 SSRs were used for validation, of which 74 produced amplification products of expected size. Genetic diversity of 30 black pepper accessions using 50 SSRs revealed four distinct clusters. Further, the cross species transferability of the SSRs was checked in nine other Piper species. Out of 50 SSRs used, 19 and 31 SSRs were amplified in nine and seven species, respectively. Thus the identified SSRs may have application in other species of the genus Piper where genome sequence is not available yet. Present study reports the first NGS based genomic SSRs in black pepper and thus constitute a valuable resource for a whole fleet of applications in genetics and plant breeding studies such as genetic map construction, QTL identification, map-based gene cloning, marker-assisted selection and evolutionary studies in Piper nigrum and related species. [ABSTRACT FROM AUTHOR]

Yellow mosaic virus disease is one of the major diseases of soybean in India. Genetic basis of 41 soybean genotypes varying in resistance against yellow mosaic virus was studied using 58 simple sequence repeat primers. A total of 140 alleles with an average of 2.41 alleles per locus were detected, which indicated very narrow genetic base of the genotypes studied. The polymorphic information content varied from 0.00 to 0.754 with an average of 0.357. Unweighted Pair Group Method with Arithmetic Average allocated the genotypes in 2 major clusters separated at 41% similarity with fairly good bootstrap support. Ten unique alleles observed in the study can be used for identification of genotype possessing that particular unique allele. The resistant group comprised of 21 genotypes with similarity coefficient 0.33 to 0.805, of which 20 genotypes were classified in a single sub-cluster. The results presented are of significance with regard to the identification of suitable donor parents for incorporating yellow mosaic resistance into popular soybean varieties. Genetically diverse parents with varying resistance against yellow mosaic virus identified in the study can be used for generating mapping population for the identification of SSR markers closely linked with yellow mosaic virus. [ABSTRACT FROM AUTHOR]

This genetic diversity study aimed to estimate the population structure and explore the use of association mapping strategies to identify linked markers for bacterial resistance, growth and fruit quality in pomegranate collections from India. In total, 88 accessions including 37 cultivated types were investigated. A total of 112 alleles were amplified by use of 44 publicly available microsatellites for estimating molecular genetic diversity and population structure. Neighbor-joining analysis, model-based population structure and principal component analysis corroborated the genetic relationships among wild-type and cultivated pomegranate collections from India. Our study placed all 88 germplasm into four clusters. We identified a cultivated clade of pomegranates in close proximity to Daru types of wild-type pomegranates that grow naturally near the foothills of the Himalayas. Admixture analysis sorted various lineages of cultivated pomegranates to their respective ancestral forms. We identified four linked markers for fruit weight, titratable acidity and bacterial blight severity. PGCT001 was found associated with both fruit weight and bacterial blight, and the association with fruit weight during both seasons analyzed was significant after Bonferroni correction. This research demonstrates effectiveness of microsatellites to resolve population structure among the wild and cultivar collection of pomegranates and future use for association mapping studies. [ABSTRACT FROM AUTHOR]

Drought tolerance was investigated in 'C306', one of the most drought tolerant wheat cultivars bred in India in the 1960's. An intervarietal mapping population of recombinant inbred lines of the cross 'C306' × 'HUW206' was evaluated for drought tolerance components, namely potential quantum efficiency of photosystem (PS) II (F/F), chlorophyll content (Chl), flag leaf temperature (Lt), and grain yield per plant (Gyp) under stress. Three independent experiments were conducted under well-watered and water-stressed conditions in greenhouses and growth chambers at Kansas State University (USA). Five hundred and sixty microsatellite markers covering the entire genome were screened for polymorphism between the parents. A QTL ( QLt.ksu- 1D) for Lt (low flag leaf temperature under stress) on the short arm of chromosome 1D between markers Xbarc271 and Xgwm337 at LOD 3.5 explained 37% of the phenotypic variation. A QTL for F/F ( QF /F .ksu- 3B) and Chl ( QChl.ksu- 3B) controlling quantum efficiency of PS II and chlorophyll content under stress were co-localized on chromosome 3B in the marker interval Xbarc68-X barc101 and explained 35-40% of the phenotypic variation for each trait. A QTL ( QGyp.ksu- 4A) for Gyp on chromosome 4A at a LOD value of 3.2 explained 16.3% of the phenotypic variation. Inconsistent QTLs were observed for F/F on chromosomes 3A, 6A, 2B, 4B, and 4D; for Chl on 3A, 6A, 2B and 4B; and for Lt on 1A, 3A 6A, 3B and 5B. The identified QTLs give a first glimpse of the genetics of drought tolerance in C306 and need to be validated in field experiments using the marker-phenotype linkages reported here. [ABSTRACT FROM AUTHOR]

In bread wheat, single-locus and two-locus QTL analyses were conducted for seven yield and yield contributing traits using two different mapping populations (P I and P II). Single-locus QTL analyses involved composite interval mapping (CIM) for individual traits and multiple-trait composite interval mapping (MCIM) for correlated yield traits to detect the pleiotropic QTLs. Two-locus analyses were conducted to detect main effect QTLs (M-QTLs), epistatic QTLs (E-QTLs) and QTL × environment interactions (QE and QQE). Only a solitary QTL for spikelets per spike was common between the above two populations. HomoeoQTLs were also detected, suggesting the presence of triplicate QTLs in bread wheat. Relatively fewer QTLs were detected in P I than in P II. This may be partly due to low density of marker loci on P I framework map (173) than in P II (521) and partly due to more divergent parents used for developing P II. Six QTLs were important which were pleiotropic/coincident involving more than one trait and were also consistent over environments. These QTLs could be utilized efficiently for marker assisted selection (MAS). [ABSTRACT FROM AUTHOR]

Powdery mildew (PM) is one of the important foliar diseases of mungbean. Resistance sources have been identified in India and the inheritance studies showed that complete resistance (RO) was controlled by two dominant genes, Pm1, Pm2. The breakdown of complete resistance (RO) into moderate resistance (R2) by race-2 (Akola) has been reported. It is assumed that the change in resistance reaction is due to a mutation in the pathogen. The present investigation was carried out with a view to screen germplasm, cultivars and mutants for identification of complete resistance (RO) sources against race-2 and to study their inheritance. ‘Mulmarada’, a local mungbean cultivar from Maharashtra state of India was identified as a complete resistance (RO) source for race-2. The inheritance of Mulmarada’s resistance (RO) was studied. The F1 and the segregation in F2 and F3 showed that the complete resistance (RO) in ‘Mulmarada’ is controlled by a single dominant gene, which is different from the earlier identified Pm1 and Pm2 resistance genes. Mulmarada’s resistance gene is designated as Pm3 for PM resistance. [ABSTRACT FROM AUTHOR]

The article discusses the role of biotechnology in improving the yield of biofuel oilseed crops such as jatropha to increase biodiesel production in India. It cited that information from the elite mapping population data could be used to screen germplasm of jatropha in order to identify DNA markers or major quantitative trait loci (QTLs) associated with high yield. It states that information gathered from model systems may be applied to improve oil content in tree species.