S. Gopala Krishnan

Molecular breeding for the development of multiple disease resistance in Basmati rice

Marker assisted backcross breeding for combining three resistance genes (xa13 and Xa21 for Bacterial Blight, Pi54 for blast) and a major QTL (qSBR11-1 for resistance to Sheath blight) in Basmati rice.

Improvement of Basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding.

Marker assisted backcross breeding was employed to incorporate the blast resistance genes, Pi2 and Pi54 and bacterial blight (BB) resistance genes xa13 and Xa21 into the genetic background of Pusa Basmati 1121 (PB1121) and Pusa Basmati 6. Foreground selection for target gene(s) was followed by arduous phenotypic and background selection which fast-tracked the recovery of recurrent parent genome (RPG) to an extent of 95.8% in one of the near-isogenic lines (NILs) namely, Pusa 1728-23-33-31-56, which also showed high degree of resemblance to recurrent parent, PB6 in phenotype. The phenotypic selection prior to background selection provided an additional opportunity for identifying the novel recombinants viz., Pusa 1884-9-12-14 and Pusa 1884-3-9-175, superior to parental lines in terms of early maturity, higher yield and improved quality parameters. There was no significant difference between the RPG recovery estimated based on SSR or SNP markers, however, the panel of SNPs markers was considered as the better choice for background selection as it provided better genome coverage and included SNPs in the genic regions. Multi-location evaluation of NILs depicted their stable and high mean performance in comparison to the respective recurrent parents. The Pi2+Pi54 carrying NILs were effective in combating a pan-India panel of Magnaporthe oryzae isolates with high level of field resistance in northern, eastern and southern parts of India. Alongside, the PB1121-NILs and PB6-NILs carrying BB resistance genes xa13+Xa21 were resistant against Xanthomonas oryzae pv. oryzae races of north-western, southern and eastern parts of the country. Three of NILs developed in this study, have been promoted to final stage of testing during the ​Kharif 2015 in the Indian National Basmati Trial.

Australian Wild Rice Reveals Pre-Domestication Origin of Polymorphism Deserts in Rice Genome

Background Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. Results We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58Mbp region on chromosome 5, which suggests that some of the ‘polymorphism deserts’ in this and other parts of the rice genome may have originated prior to domestication due to natural selection. Conclusions Analysis of genes in the ‘polymorphism deserts’ indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Distribution and extent of diversity in Cucumis species in the Aravalli ranges of India

Among the 52 species reported in Cucumis, cucumber and muskmelon are the most important species, extensively cultivated by the human for consumption. Diversity has been reported in the wild species of Cucumis from India. Considering the status of genetic erosion of the variability in the various species of Cucumis, a total of 121 germplasm accessions of five different Cucumis species were collected through three explorations in the parts of Aravalli ranges of northwestern India. The paper presents the distribution, collection, extent of variability, associated indigenous traditional knowledge, conservation status of these Cucumis species and prospects of their utilization in crop improvement.

Improving Salt Tolerance in Rice: Looking Beyond the Conventional

Several factors in the intensive cropping system have played significant role in deteriorating soil health in general. soil salinization is one of the major issues threatening crop productivity in major irrigated rice growing areas of the world. Salinity is a serious issue in rice, the crop that feeds half the world, since it is sensitive to salt accumulation. With the world population growing incessantly, there is an urgent need to increase rice productivity especially in salinized lands as well as to reutilize lands that are rendered unproductive due to salt accumulation. It is therefore essential to develop varieties that are phenologically capable of sustaining excess salt throughout its life span and produce higher yield. Although there is sufficient variability in rice germplasm for salt tolerance, conventional breeding has been far less fruitful in addressing this complex problem. With the deeper understanding of the intricate mechanisms of salt tolerance and the array of genes and useable quantitative trait loci that are being discovered, the breeding scenario towards salt tolerant rice is poised to take a more productive turn in near future. This chapter outlines the latest developments in rice breeding towards salt tolerance through employment of modern molecular techniques in conjunction with the conventional breeding approaches.

Primitive weedy forms of guar, adak guar: possible missing link in the domestication of guar [Cyamopsis tetragonoloba (L.) Taub.]

Crop domestication has lead to the selection of a wide range of traits that distinguish domesticated crops from their wild ancestors. Over the past four decades, concerted efforts by archaeologists and geneticists have provided novel insights into the domestication of crops. However, minor crops are rarely a subject for intensive domestication studies and very less is known on the domestication of guar [Cyamopsis tetragonoloba (L.) Taub.] except the trans-domestication hypothesis. The hypothesis proposes that the domestication of guar took place in recent times in the dry areas of the northwestern region of Indo-Pakistan subcontinent and the African wild species, C. senegalensis Guill. et Perr., as its ancestor. However, the process by which the wild species was domesticated is not fully understood. The present paper describes the exploration, collection and in situ characterization of the primitive weedy forms of guar that could be the missing link between the wild and cultivated species. Adak guar is found to grow along with cultivated guar as a weed and is characterized by several primitive characters, prominent among which are spreading habit, small inedible pods which shatter at maturity, hard seed coat and seed dormancy. A total of 66 germplasm collections of these primitive weedy forms of guar have been made from naturally occurring populations in the arid regions of northwestern India. Systematic studies involving these primitive weedy forms can help in understanding the domestication bottlenecks and in utilizing the genetic variation lost during the process of domestication for the improvement of cultivated guar.

Understanding Host-Pathogen Interactions with Expression Profiling of NILs Carrying Rice-Blast Resistance Pi9 Gene

Magnaporthe oryzae infection causes rice blast, a destructive disease that is responsible for considerable decrease in rice yield. Development of resistant varieties via introgressing resistance genes with marker-assisted breeding can eliminate pesticide use and minimize crop losses. Here, resistant near-isogenic line (NIL) of Pusa Basmati-1(PB1) carrying broad spectrum rice blast resistance gene Pi9 was used to investigate Pi9-mediated resistance response. Infected and uninfected resistant NIL and susceptible control line were subjected to RNA-Seq. With the exception of one gene (Pi9), transcriptional signatures between the two lines were alike, reflecting basal similarities in their profiles. Resistant and susceptible lines possessed 1043 (727 up-regulated and 316 down-regulated) and 568 (341 up-regulated and 227 down-regulated) unique and significant differentially expressed loci (SDEL), respectively. Pathway analysis revealed higher transcriptional activation of kinases, WRKY, MYB, and ERF transcription factors, JA-ET hormones, chitinases, glycosyl hydrolases, lipid biosynthesis, pathogenesis and secondary metabolism related genes in resistant NIL than susceptible line. Singular enrichment analysis demonstrated that blast resistant NIL is significantly enriched with genes for primary and secondary metabolism, response to biotic stimulus and transcriptional regulation. The co-expression network showed proteins of genes in response to biotic stimulus interacted in a manner unique to resistant NIL upon M. oryzae infection. These data suggest that Pi9 modulates genome-wide transcriptional regulation in resistant NIL but not in susceptible PB1. We successfully used transcriptome profiling to understand the molecular basis of Pi9-mediated resistance mechanisms, identified potential candidate genes involved in early pathogen response and revealed the sophisticated transcriptional reprogramming during rice-M. oryzae interactions.

Marker Aided Incorporation of Saltol, a Major QTL Associated with Seedling Stage Salt Tolerance, into Oryza sativa ‘Pusa Basmati 1121’

Pusa Basmati 1121 (PB1121), an elite Basmati rice cultivar is vulnerable to salinity at seedling stage. A study was undertaken to impart seedling-stage salt tolerance into PB1121 by transferring a quantitative trait locus (QTL), Saltol, using FL478 as donor, through marker assisted backcrossing. Sequence tagged microsatellite site (STMS) marker RM 3412, tightly linked to Saltol was used for foreground selection. Background recovery was estimated using 90 genome-wide STMS markers. Systematic phenotypic selection helped in accelerated recovery of recurrent parent phenome (RPP). A set of 51 BC3F2 lines homozygous for Saltol were advanced to develop four improved near isogenic lines (NILs) of PB1121 with seedling stage salt tolerance. The background genome recovery in the NILs ranged from 93.3 to 99.4%. The improved NILs were either similar or better than the recurrent parent PB1121 for yield, grain and cooking quality and duration. Biochemical analyses revealed significant variation in shoot and root Na+ and K+ concentrations. Correlation between shoot and root Na+ concentration was stronger than that between root and shoot K+ concentration. The effect of QTL integration into the NILs was studied through expression profiling of OsHKT1;5, one of the genes present in the Saltol region. The NILs had significantly higher OsHKT1;5 expression than the recurrent parent PB1121, but lower than FL478 on salt exposure validating the successful introgression of Saltol in the NILs. This was also confirmed under agronomic evaluation, wherein the NILs showed greater salt tolerance at seedling stage. One of the NILs, Pusa1734-8-3-3 (NIL3) showed comparable yield and cooking quality to the recurrent parent PB1121, with high field level seedling stage salinity tolerance and shorter duration. This is the first report of successful introgression of Saltol into a Basmati rice cultivar.

Morphological variability in holy basil (Ocimum tenuiflorum L.) from India

Forty-nine accessions of cultivated holy basil (Ocimum tenuiflorum L.) representing four phytogeographical regions of India were characterized for 18 qualitative and 14 quantitative traits using minimal descriptors developed by the National Bureau of Plant Genetic Resources with minor modifications. Dendrograms were constructed using Ward’s Minimum Variance method. Analysis showed high degree of variation among studied accessions indicating rich diversity represented within the populations from different phytogeographical regions and relatedness among the morphotypes.

Molecular mapping of grain physico-chemical and cooking quality traits using recombinant inbred lines in rice (Oryza sativa L.)

A recombinant inbred line (RIL) population derived from the cross between Pusa1266 (a new plant type) with Jaya (a popular indica rice variety) was used for mapping QTL associated with grain physico-chemical and cooking quality traits in rice. A total of 310 recombinant inbred lines were evaluated for nine grain physico-chemical and cooking quality traits at two locations in India, during Kharif 2007. A linkage map based on 135 molecular markers was developed and a total of 22 QTL associated with seven traits, namely brown rice percentage, milled rice percentage, kernel length before cooking, kernel breadth before cooking, length/breadth ratio, kernel length after cooking and kernel breadth after cooking on seven different chromosomes were identified by composite interval mapping. Pusa1266 allele contributed positively at 14 loci whereas Jaya contributed at 8 loci. Nine QTL influencing five different traits were identified with an R2 > 10%. A marker interval RM18222–HvSSR05-39 on chromosome 5 influencing two traits (qKBBC5-1, qLBR5-1) across the locations was identified. This locus can be used for fine mapping and identification of the candidate gene for these traits.