Genetics and Genomics of Bacterial Blight Resistance in Rice

Rice is an important food crop for half the world’s population and has been in cultivation for over 10,000 years. During the last few decades, rice has evolved intricate relationships with associated pathogens and pests, bacterial blight (BB) being one of the most important among them. Utilization of resistant varieties with agricultural management practices is a more effective way to control BB. Of the 42 different resistance (R) genes identified to confer BB resistance, 9 have been isolated and cloned, whereas a few of the avirulence genes and a large number of candidate pathogenicity genes have been isolated from Xanthomonas oryzae pv. oryzae. The complete genome sequences of two different rice subspecies japonica and indica and three different races of BB pathogen are available. Therefore, the interaction between rice-Xoo could be deciphered and pave a way to study the molecular aspects of bacterial pathogenesis and host counter measures like innate immunity and R gene–mediated immunity. Although several of the type III effectors of Xoo have been characterized and the host targets of a few of them identified, a relatively large number of candidate effectors remain to be studied and their functional analysis may provide key for developing broad spectrum and durable resistance to BB

Species diversity of genus Capsicum using agromorphological descriptors and simple sequence repeat markers

906-915Sustainability of crops in most demand depends upon their genetic diversity. Capsicum, commonly called chilli, is one such crop with its fruits extensively used as vegetable across the world. Knowledge on various traits is important for genetic improvement of such species. Here, we assessed the genetic diversity among 10 genotypes of six Capsicum species, namely Capsicum annuum, C. chinense, C. chacoense, C. frutescens, C. tovarii and C. galapagoense. C. annuum MS-12 is a genetic male sterile line. We used morphological descriptors and simple-sequence repeat (SSR) molecular markers for this study. Out of 60 SSR screened, 22 markers (36.66%) showed polymorphism. Alleles number per locus varied from 3 to 7. Average PIC value for 22 polymorphic markers was 0.69, and ranged from 0.54 for the primer Hpms 1-139 to 0.85 for the primer CAMS-072. Ten genotypes of Capsicum species were grouped into three major clusters such that genotypes in a single cluster had less dissimilarity matrix values among themselves than which belongs to other clusters. Range of fruit weight and pericarp thickness varied from 0.1 g (‘PAU-621’) to 2.3 g (‘MS-12’), and from 0.29 mm (‘PAU-621’) to1.09 mm (‘MS12’), respectively. These two genotypes can be used in hybridization or in recombinant breeding program for obtaining higher heterotic effects/ heterosis or for transgressive segregants in chilli pepper

Species diversity of genus Capsicum using agromorphological descriptors and simple sequence repeat markers

Sustainability of crops in most demand depends upon their genetic diversity. Capsicum, commonly called chilli, is one such crop with its fruits extensively used as vegetable across the world. Knowledge on various traits is important for genetic improvement of such species. Here, we assessed the genetic diversity among 10 genotypes of six Capsicum species, namely Capsicum annuum, C. chinense, C. chacoense, C. frutescens, C. tovarii and C. galapagoense. C. annuum MS-12 is a genetic male sterile line. We used morphological descriptors and simple-sequence repeat (SSR) molecular markers for this study. Out of 60 SSR screened, 22 markers (36.66%) showed polymorphism. Alleles number per locus varied from 3 to 7. Average PIC value for 22 polymorphic markers was 0.69, and ranged from 0.54 for the primer Hpms 1-139 to 0.85 for the primer CAMS-072. Ten genotypes of Capsicum species were grouped into three major clusters such that genotypes in a single cluster had less dissimilarity matrix values among themselves than which belongs to other clusters. Range of fruit weight and pericarp thickness varied from 0.1 g (‘PAU-621’) to 2.3 g (‘MS-12’), and from 0.29 mm (‘PAU-621’) to1.09 mm (‘MS- 12’), respectively. These two genotypes can be used in hybridization or in recombinant breeding program for obtaining higher heterotic effects/ heterosis or for transgressive segregants in chilli pepper

Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize

Maize is the third most important cereal crop worldwide. However, its production is vulnerable to heat stress, which is expected to become more and more severe in coming years. Germplasm resilient to heat stress has been identified, but its underlying genetic basis remains poorly understood. Genomic mapping technologies can fill the void, provided robust markers are available to tease apart the genotype-phenotype relationship. In the present investigation, we used data from an RNA-seq experiment to identify single nucleotide polymorphisms (SNPs) between two contrasting lines, LM11 and CML25, sensitive and tolerant to heat stress, respectively. The libraries for RNA-seq were made following heat stress treatment from three separate tissues/organs, comprising the top leaf, ovule, and pollen, all of which are highly vulnerable to damage by heat stress. The single nucleotide variants (SNVs) calling used STAR mapper and GATK caller pipelines in a combined approach to identify highly accurate SNPs between the two lines. A total of 554,423, 410,698, and 596,868 SNVs were discovered between LM11 and CML25 after comparing the transcript sequence reads from the leaf, pollen, and ovule libraries, respectively. Hundreds of these SNPs were then selected to develop into genome-wide Kompetitive Allele-Specific PCR (KASP) markers, which were validated to be robust with a successful SNP conversion rate of 71%. Subsequently, these KASP markers were used to effectively genotype an F2 mapping population derived from a cross of LM11 and CML25. Being highly cost-effective, these KASP markers provide a reliable molecular marker toolkit to not only facilitate the genetic dissection of the trait of heat stress tolerance but also to accelerate the breeding of heat-resilient maize by marker-assisted selection (MAS)

Genetic Diversity Among <i>Colletotrichum falcatum</i> Isolates Causing Red Rot of Sugarcane in Subtropical Region of India

Silver Genetic diversity of Colletotrichum falcatum causing red rot of sugarcane was assessed based on morphological, pathological and molecular characteristics especially from sub-tropical Indian conditions. Sixteen isolates of this pathogen were collected based on the extensive survey on prominent varieties grown in the region along with some elite selections. Morphological observations (colony colour, mycelium pattern and sporulation) grouped the isolates into two distinct types (C1: light type and C2: dark type). However, quantitative data on colony diameter showed five clusters for these isolates. Pathogenic characterization of these isolates on fourteen standard differentials formed six groups, ingroup 1: (CF-Pb-1) isolates Cf-157, Cf-249 and Cf-248 were the most virulent while group 6 (CF-Pb-6) isolates Cf-60 and Cf-247 were the least one. The genetic relatedness among the isolates using Random Amplified Polymorphic DNA (RAPD) analysis revealed sufficient molecular polymorphism, which in turn confirmed the variation in virulence of different isolates. The data categorized different isolates into two major clusters and five independent lineages. Polymorphic information content (PIC) ranged from 0.701 to 0.929. Isolate Cf-223 was found to be genetically most diverse among all the isolates. Present study inferred that morphological grouping of most of the isolates showed positive correlation with the pathogenic variability while molecular diversity did not showed such associations

Banded leaf and sheath blight: threat to maize

Not AvailableBanded leaf and sheath blight (BLSB) is a destructive disease of maize and it leads to 100 per cent yield losses. The causal organism of BLSB is Rhizoctonia solani and the organism grows under favourable humidity (88–90 per cent) and temperature (15–35o C) conditions. The management practices used to control the disease spread are inadequate at this moment due to its broad host range. Therefore, the identification and exploitation of genetic resistance is an economical and sustainable option to control this disease. However, limited genetic variability poses a major challenge for resistance breeding against BLSB in maize. A few resistant sources have been identified and used for the identification of QTLs and candidate genes responsible for BLSB resistance. Here, we summarized the management practices, genetic resources, and different molecular approaches used to identify the QTLs and key candidate genes associated with BLSB resistance in maizeNot Availabl

DNA-free genome editing for ZmPLA1 gene via targeting immature embryos in tropical maize

ABSTRACTDoubled haploid (DH) production accelerates the development of homozygous lines in a single generation. In maize, haploids are widely produced by the use of haploid inducer Stock 6, earlier reported in 1959. Three independent studies reported haploid induction in maize which is triggered due to a 4 bp frame-shift mutation in matrilineal (ZmPLA1) gene. The present study was focused on the generation of mutants for ZmPLA1 gene in maize inbred line LM13 through site-directed mutagenesis via CRISPR/Cas9-mediated ribonucleoprotein (RNP) complex method to increase the haploid induction rate. Three single guide RNAs (sgRNAs) for the ZmPLA1 gene locus were used for transforming the 14 days old immature embryos via bombardment. 373 regenerated plants were subjected to mutation detection followed by Sanger’s sequencing. Out of three putative mutants identified, one mutant depicted one base pair substitution and one base pair deletion at the target site

Genome wide association mapping for heat tolerance in sub-tropical maize

Not AvailableHeat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program.An association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology. The present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines.Not Availabl

Identification of genomic regions associated with shoot fly resistance in maize and their syntenic relationships in the sorghum genome.

Shoot fly (Atherigona naqvii) is one of the major insects affecting spring maize in North India and can cause yield loss up to 60 per cent. The genetics of insect resistance is complex as influenced by genotypic background, insect population and climatic conditions. Therefore, quantitative trait loci (QTL) mapping is a highly effective approach for studying genetically complex forms of insect resistance. The objective of the present study was to dissect the genetic basis of resistance and identification of genomic regions associated with shoot fly resistance. A total of 107 F2 population derived from the cross CM143 (resistant) x CM144 (susceptible) was genotyped with 120 SSR markers. Phenotypic data were recorded on replicated F2:3 progenies for various component traits imparting resistance to shoot fly at different time intervals. Resistance to shoot fly was observed to be under polygenic control as evidenced by the identification of 19 putative QTLs governed by overdominance to partial dominance and additive gene actions. The major QTLs conditioning shoot fly resistance viz., qDH9.1 (deadheart) and qEC9.1 (oviposition) explaining 15.03 and 18.89 per cent phenotypic variance, respectively were colocalized on chromosome 9. These QTLs are syntenic to regions of chromosome 10 of sorghum which were also accounted for deadheart and oviposition suggesting that the same gene block may be responsible for shoot fly resistance. The candidate genes such as cysteine protease, subtilisin-chymotrypsin inhibitor, cytochrome P450 involved in synthesis of alleochemicals, receptor kinases, glossy15 and ubiquitin-proteasome degradation pathway were identified within the predicted QTL regions. This is the first reported mapping of QTLs conferring resistance to shoot fly in maize, and the markers identified here will be a valuable resource for developing elite maize cultivars with resistance to shoot fly

Not Available

Not AvailableWild relatives of rice (Oryza sativa) are important sources for rice improvement under both biotic and abiotic stress. Sheath blight caused by Rhizoctonia solani [Teleomorph - Thanatephorus cucumeris (Frank) Donk.] is major rice (Oryza sativa L.) disease and cause significant losses up to 69% under favourable environmental conditions worldwide. Four hundred five accessions of Oryza rufipogon were screened to identify resistance against sheath blight during the year 2015.There was not a single accession which showed complete resistance. Out of 405, 22 were found to be moderately resistant which were further evaluated during the years 2016 and 2017. Finally 19 accessions were identified as promising one which showed continuously moderately resistant reaction for three years. Correlation study revealed that the different disease variables such as lesion height, relative lesion height and disease score measured were significantly (P<0.05) correlated. All the genotypes and genotype*experiment interaction had a significant (P < 0.001) effect on all the disease variables. Cluster analysis showed that all the accessions were clustered into 4 groups during the year 2015. These groups showed moderately resistant, moderately susceptible and susceptible reaction. The results of present study showed the promising accessions viz., IRGC80600, IRGC80762, IRGC104404A, CR100036 and CR100436 can be utilized in the sheath blight resistance breeding programme.Not Availabl