J. C. Rana

mQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea.

The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8–10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (CaqaPN4.1: 867.8 kb and CaqaPN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (CaqbPN4.1: 637.5 kb and CaqbPN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea.

Comparative Agronomic Performance and Reaction to Fusarium wilt of Lens culinaris × L. orientalis and L. culinaris × L. ervoides derivatives

The development of transgressive phenotype in the segregating populations has been speculated to contribute to niche divergence of hybrid lineages, which occurs most frequently at larger genetic distances. Wild Lens species are considered to be more resistant against major biotic and abiotic stresses than that of the cultivated species. In the present study, we assessed the comparative agronomic performance of lentil (Lens culinaris subsp. culinaris) inter-sub-specific (L. culinaris subsp. orientalis) and interspecific (L. ervoides) derivatives, also discussed its probable basis of occurrence. The F3, F4, and F5 inter sub-specific and interspecific populations of ILL8006 × ILWL62 and ILL10829 × ILWL30, respectively revealed a substantial range of variation for majority of agro-morphological traits as reflected by the range, mean and coefficient of variation. A high level of fruitful heterosis was also observed in F3 and F4 progeny for important traits of interest. Phenotypic coefficient of variation (PCV) was higher in magnitude than genotypic coefficient of variation (GCV) in all generations for several quantitative characters. The results showed high heritability estimates for majority of traits in conjunction with low to high genetic advance in F3 and F4 generations. Further, F5 progeny of ILL10829 × ILWL30, manifested resistant disease reaction for fifteen recombinant inbred lines (RILs) against (Fusarium oxysporum f. sp. lentis (Vasd. Srin.) Gord.). The multilocation agronomic evaluation of both crosses showed better results for earliness, desirable seed yield and Fusarium wilt resistance under two agro-ecological regions of north-western India. These better performing recombinants of ILL8006 × ILWL62 and ILL10829 × ILWL30 can be advanced for further genetic improvement and developing high yielding disease resistant cultivars of lentil.

The Prehistoric Indian Ayurvedic Rice Shashtika Is an Extant Early Domesticate With a Distinct Selection History

Fully domesticated rice is considered to have emerged in India at approximately 2000 B.C., although its origin in India remains a contentious issue. The fast-growing 60-days rice strain described in the Vedic literature (1900–500 B.C.) and termed Shashtika (Sanskrit) or Njavara (Dravidian etymology) in Ayurveda texts including the seminal texts Charaka Samhita and Sushruta Samhita (circa 660–1000 B.C.) is a reliable extant strain among the numerous strains described in the Ayurveda literature. We here report the results of the phylogenetic analysis of Njavara accessions in relation to the cultivars belonging to the known ancestral sub-groups indica, japonica, aromatic, and aus in rice gene pool and the populations of the progenitor species Oryza rufipogon using genetic and gene genealogical methods. Based on neutral microsatellite markers, Njavara produced a major clade, which comprised of minor clades corresponding to the genotypic classes reported in Njavara germplasm, and was distinct from that were produced by the ancestral sub-groups. Further we performed a phylogenetic analysis using the combined sequence of 19 unlinked EST-based sequence tagged site (STS) loci with proven potential in inferring rice phylogeny. In the phylogenetic tree also the Njavara genotypic classes were clearly separated from the ancestral sub-groups. For most loci the genealogical analysis produced a high frequency central haplotype shared among most of the rice samples analyzed in the study including Njavara and a set of O. rufipogon accessions. The haplotypes sharing pattern with the progenitor O. rufipogon suggests a Central India–Southeast Asia origin for Njavara. Results signify that Njavara is genetically distinct in relation to the known ancestral sub-groups in rice. Further, from the phylogenetic features together with the reported morphological characteristics, it is likely that Njavara is an extant early domesticate in Indian rice gene pool, preserved in pure form over millennia by the traditional prudence in on-farm selection using 60-days maturity, because of its medicinal applications.

Identification and evaluation of Indian mustard genotypes for white rust resistance and agronomic performance

The screening of 2000 Indian mustard accessions against white rust and phenotypic evaluation of resistant accessions to assess the nature and magnitude of genetic diversity including their agronomic potential was carried out at three locations during rabi of 2014–2016. Out of 2000 germplasm accessions, 168, 46 and 185 accessions were found resistant at Ludhiana, Pantnagar, and Hissar, respectively but only 27 were identified as resistant across the locations indicating the pathogenic variability at different locations. These 27 accessions were further validated under artificial inoculation and eight of them, namely, IC265495, IC313380, EC766091, EC766133, EC766134, EC766192, EC766230 and EC766272 were identified as highly resistant with disease severity reaction (PDI = 0) to A. candida at both cotyledonary and true leaf stages. Agronomic evaluation of these 27 accessions facilitated the identification of superior genotypes with high magnitude of genetic diversity for their use in breeding. As compared to check varieties, elite genotype(s) such as IC313380 was found promising for days to flowering (40), silique on main stem (52.6), silique length (4.2 cm), seeds per silique (17.2) and oil content (41.4%); EC766230 for no. of primary branches (8), seeds/silique (16.8), seed yield/plant (16.0g), oil content (38.7%) while EC766272 for silique on main stem (55.50), seed yield/plant (18g) and oil content (40.5%). The resistant accessions coupled with agronomic superiority may be useful genetic resources for improvement of Indian mustard. In addition, the resistant accessions can serve as a rich gene pool for breeding programmes.

Foxtail and Barnyard Millets

Millets comprise group of crops which can play a major role in achieving the goal of nutritional security through diversification of diets in spite that these are generally grown in marginal and infertile lands. Compared to major cereals, millets provide carbohydrates, protein, minerals, dietary fibre, vitamins and various functional molecules to the people residing in Asian and African subcontinents. Among the small-grained millets, foxtail and barnyard millets are of short duration, drought resistant and widely grown crops. The availability of genome-wide sequences in foxtail millet has shifted the pace towards development of different kind of markers and linkage mapping. In contrary, little or no genomic work has been done in barnyard millet. But using comparative genomics from available foxtail sequences, different markers and QTLs can be identified in barnyard millet also. This chapter also covers the interspecific hybridisation, barriers to interspecific hybridisation and conventional and contemporary approaches used for the development of interspecific hybridisation. Further, in foxtail and barnyard millets, genetic-based broadening is required for agronomic traits particularly yield-related traits, resistance to biotic and abiotic stresses and nutritional traits.

Genetic Resources of Buckwheat in India

Abstract Diverse agroclimatic niches in the Indian Himalayan region support a wide range of genetic diversity in buckwheat species. Buckwheat has multiple uses as grain and green leafy vegetable and is known to be rich in many major and minor nutrients. About 23 species occur in the highlands of the Euro-Asia region, and two of them, namely, Fagopyrum esculentum and Fagopyrum Tataricum, are cultivated while others occur wild or as weeds. The germplasm comprising 1055 germplasm accessions has been conserved ex situ at the National Bureau of Plant Genetic Resources. The entire collection has been evaluated for various traits and several trait-specific reference sets have been developed for enhanced use in breeding programs for the understanding of molecular dynamics of various genes involved in the biosynthesis of flavnoids such as rutin. cDNA-amplified fragment length polymorphism technology was successfully utilized to capture genes that are contributing to differences in rutin content in seed maturing stages. Gene-specific sequence tagged site markers and their possible association with phenotypic traits in buckwheat has also been established. Tartary buckwheat contains approximately 40 times more rutin than common buckwheat, therefore it is more important for industrial considerations. Buckwheat has a poor repertoire of genetic markers that could be employed for its genetic improvement, despite its industrial importance. Comparative genomics of rutin biosynthesis genes is being investigated by utilizing sequences from other plant species where these genes have been characterized. Lack of advanced processing technology has limited value-adding opportunities for meeting market demand, thus efforts should be focused on developing value-adding opportunities for farmers and enterprises to develop more diversified products.

Chickpea genetic resources and its utilization in India: Current status and future prospects

Chickpea is recognized as most nutritious pulse crop and with respect to acreage, it ranks at the top among pulses in India. Realizing the significance of plant genetic resources, special efforts were made by the National Bureau of Plant Genetic Resources (NBPGR) to collect the chickpea germplasm from different states of India including certain useful introductions from other countries. A large number of germplasm accessions including wild species were characterized and evaluated for various agro-morphological traits using chickpea minimal descriptor. Thus, extensive germplasm collections now exist in various gene banks of the world including India. As far as germplasm maintenance is concerned, a core set developed by ICRISAT comprising of 1956 accessions and mini core set of 211 accessions representing diversity for seed yield and its component traits. Further, core set developed by NBPGR consisting of 1103 accessions extracted from 14651 accessions conserved in the Indian National Gene Bank revealed that 70% of materials belong to Indian origin. The characterization and evaluation experiments of chickpea conducted across the country led to the registration of some unique germplasm accessions for different trait of interest. However, using crop wild relatives, several interspecific crosses and advance pre-breeding lines were developed by the pulse research institutions in India. The trait of interest incorporated especially from C. reticulatum, C. echinospermum and C. judaicum species for widening the genetic base of cultivated gene pool. Some pre-breeding lines have been suggested as useful donors in national chickpea crossing programmes.