Single nucleotide polymorphism (SNP) is the most abundant DNA sequence variation present in plant genomes. Here, we report the design and validation of a unique genic-SNP genotyping chip for genetic and evolutionary studies as well as molecular breeding applications in rice. The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes. Assays with this chip showed high success rate and reproducibility because of the SC gene based array with no sequence redundancy and cross-hybridisation problems. The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated. Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.

Pigeonpea (Cajanus cajan (L.) Millsp.) is a major food legume cultivated in semi-arid tropical regions including the Indian subcontinent, Africa, and Southeast Asia. It is an important source of protein, minerals, and vitamins for nearly 20% of the world population. Due to high carbon sequestration and drought tolerance, pigeonpea is an important crop for the development of climate resilient agriculture and nutritional security. However, pigeonpea productivity has remained low for decades because of limited genetic and genomic resources, and sparse utilization of landraces and wild pigeonpea germplasm. Here, we present a dense intraspecific linkage map of pigeonpea comprising 932 markers that span a total adjusted map length of 1,411.83 cM. The consensus map is based on three different linkage maps that incorporate a large number of single nucleotide polymorphism (SNP) markers derived from next generation sequencing data, using Illumina GoldenGate bead arrays, and genotyping with restriction site associated DNA (RAD) sequencing. The genotyping-by-sequencing enhanced the marker density but was met with limited success due to lack of common markers across the genotypes of mapping population. The integrated map has 547 bead-array SNP, 319 RAD-SNP, and 65 simple sequence repeat (SSR) marker loci. We also show here correspondence between our linkage map and published genome pseudomolecules of pigeonpea. The availability of a high-density linkage map will help improve the anchoring of the pigeonpea genome to its chromosomes and the mapping of genes and quantitative trait loci associated with useful agronomic traits.

Maydis leaf blight (MLB) incited by Bipolaris maydis occurs in most of the maize growing regions. Present study revealed morphological divergence among 74 isolates of B. maydis collected from geographically distant places of India. Based on morpho-cultural features clustered by R software, 25 representative isolates of B. maydis were used for race identification. The internal transcribed spacer (ITS) sequence further confirmed the isolates as B. maydis. In recent concept, variation in disease incidence and infectivity denotes genetic shift in the pathogen or introduction of new pathogenic race(s) through germplasm exchange. For unveiling Indian race(s) of B. maydis, present exploration was made. Four genetically divergent maize genotypes with cytoplasmic male sterility (CMS), viz. -C (MGU- 161QPV-C), -T (MGU- 345PV-T), -S (MGU-150Q-S) and CM-119 (fertile cytoplasm) were assessed using 25 isolates of B. maydis during kharif 2018-19 at ICAR-IARI, New Delhi. The genotype MGU-161QPV-C associated with CMS-C was highly resistant followed by MGU-345PV-T (CMS-T) and MGU-150Q-S (CMS-S), whereas CM-119 showed high susceptibility. Present outcome confirmed prevalence of race 'O' of B. maydis in India and eliminated uncertainty about occurrence of other races, i.e. T and C.

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