GBS-Based SNP Map Pinpoints the QTL Associated With Sorghum Downy Mildew Resistance in Maize (Zea mays L.).

Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi , threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%-18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs.

Gene Pyramiding for Achieving Enhanced Resistance to Bacterial Blight, Blast, and Sheath Blight Diseases in Rice.

Bacterial blight, blast, and sheath blight are the commonest diseases causing substantial yield loss in rice around the world. Stacking of broad-spectrum resistance genes/QTLs into popular cultivars is becoming a major objective of any disease resistance breeding program. The varieties ASD 16 and ADT 43 are the two popular, high yielding, and widely grown rice cultivars of South India, which are susceptible to bacterial blight (BB), blast, and sheath blight diseases. The present study was carried out to improve the cultivars (ASD 16 and ADT 43) through introgression of bacterial blight (xa5, xa13, and Xa21), blast (Pi54), and sheath blight (qSBR7-1, qSBR11-1, and qSBR11-2) resistance genes/QTLs by MABB (marker-assisted backcross breeding). IRBB60 (xa5, xa13, and Xa21) and Tetep (Pi54; qSBR7-1, qSBR11-1, and qSBR11-2) were used as donors to introgress BB, blast, and sheath blight resistance into the recurrent parents (ASD 16 and ADT 43). Homozygous (BC3F3 generation), three-gene bacterial blight pyramided (xa5 + xa13 + Xa21) lines were developed, and these lines were crossed with Tetep to combine blast (Pi54) and sheath blight (qSBR7-1, qSBR11-1, and qSBR11-2) resistance. In BC3F3 generation, the improved pyramided lines carrying a total of seven genes/QTLs (xa5 + xa13 + Xa21 + Pi54 + qSBR7-1 + qSBR11-1 + qSBR11-2) were selected through molecular and phenotypic assay, and these were evaluated for resistance against bacterial blight, blast, and sheath blight pathogens under greenhouse conditions. We have selected nine lines in ASD 16 background and 15 lines in ADT 43 background, exhibiting a high degree of resistance to BB, blast, and sheath blight diseases and also possessing phenotypes of recurrent parents. The improved pyramided lines are expected to be used as improved varieties or used as a potential donor in breeding programs. The present study successfully introgressed Pi54, and qSBR QTLs (qSBR7-1, qSBR11-1, and qSBR11-2) from Tetep and major effective BB-resistant genes (xa5, xa13, and Xa21) from IRBB60 into the commercial varieties for durable resistance to multiple diseases.

Seed Priming: A Feasible Strategy to Enhance Drought Tolerance in Crop Plants.

Drought is a serious threat to the farming community, biasing the crop productivity in arid and semi-arid regions of the world. Drought adversely affects seed germination, plant growth, and development via non-normal physiological processes. Plants generally acclimatize to drought stress through various tolerance mechanisms, but the changes in global climate and modern agricultural systems have further worsened the crop productivity. In order to increase the production and productivity, several strategies such as the breeding of tolerant varieties and exogenous application of growth regulators, osmoprotectants, and plant mineral nutrients are followed to mitigate the effects of drought stress. Nevertheless, the complex nature of drought stress makes these strategies ineffective in benefiting the farming community. Seed priming is an alternative, low-cost, and feasible technique, which can improve drought stress tolerance through enhanced and advanced seed germination. Primed seeds can retain the memory of previous stress and enable protection against oxidative stress through earlier activation of the cellular defense mechanism, reduced imbibition time, upsurge of germination promoters, and osmotic regulation. However, a better understanding of the metabolic events during the priming treatment is needed to use this technology in a more efficient way. Interestingly, the review highlights the morphological, physiological, biochemical, and molecular responses of seed priming for enhancing the drought tolerance in crop plants. Furthermore, the challenges and opportunities associated with various priming methods are also addressed side-by-side to enable the use of this simple and cost-efficient technique in a more efficient manner.

Improvement of Stable Restorer Lines for Blast Resistance through Functional Marker in Rice (Oryza sativa L.).

Two popular stable restorer lines, CB 87 R and CB 174 R, were improved for blast resistance through marker-assisted back-cross breeding (MABB). The hybrid rice development program in South India extensively depends on these two restorer lines. However, these restorer lines are highly susceptible to blast disease. To improve the restorer lines for resistance against blasts, we introgressed the broad-spectrum dominant gene Pi54 into these elite restorer lines through two independent crosses. Foreground selection for Pi54 was done by using gene-specific functional marker, Pi54 MAS, at each back-cross generation. Back-crossing was continued until BC3 and background analysis with seventy polymorphic SSRs covering all the twelve chromosomes to recover the maximum recurrent parent genome was done. At BC3F2, closely linked gene-specific/SSR markers, DRRM-RF3-10, DRCG-RF4-8, and RM 6100, were used for the identification of fertility restoration genes, Rf3 and Rf4, along with target gene (Pi54), respectively, in the segregating population. Subsequently, at BC3F3, plants, homozygous for the Pi54 and fertility restorer genes (Rf3 and Rf4), were evaluated for blast disease resistance under uniform blast nursery (UBN) and pollen fertility status. Stringent phenotypic selection resulted in the identification of nine near-isogenic lines in CB 87 R × B 95 and thirteen in CB 174 R × B 95 as the promising restorer lines possessing blast disease resistance along with restoration ability. The improved lines also showed significant improvement in agronomic traits compared to the recurrent parents. The improved restorer lines developed through the present study are now being utilized in our hybrid development program.

Advances in the Xoo-rice pathosystem interaction and its exploitation in disease management.

Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the devastating diseases of rice worldwide. The pathogen reported to cause 70% crop loss in some of the susceptible genotypes under disease favoring environments, viz., temperature ranging between 25 to 34°C and relative humidity more than 70%. In Xoo, about 245 genes govern the pathogenicity and host specificity. The hypersensitive response and pathogenicity (hrp) genes responsible for disease occurrence were clustered in the pathogenicity island of 31.3 Kb. The protein secreted through type three secretory system and type one secretory system mediates infection and establishment of the pathogen inside the host. However, elicitor molecules from Xoo triggered the resistant response in rice against the pathogen. An array of resistant genes (R genes) was known to be invoked by the host to combat the bacterial infection. To date, of the 45 Xa genes in rice, nine were cloned and characterized. The evolution of new races has made the task of developing resistant rice genotypes more challenging as it demands a comprehensive breeding strategy involving the best use of R genes from the existing gene pool. Thus, to combat the infection from the existing races and to slow down the emergence of new Xoo races, pyramiding two or more R genes was found to be effective against bacterial blight disease. In India, the successfully commercialized example includes the development of rice genotypes, viz., Improved Pusa Basmati- 1, Improved Samba Mahsuri, PR106, Type 3 Basmati, and Mahsuri with selected R genes, viz., xa5, Xa4, xa13 and Xa21 against bacterial blight resistance. This review primarily portray Xoo-rice interactions and provides opportunities for its effective management through sustainable technologies.

Improved host-plant resistance to Phytophthora rot and powdery mildew in soybean (Glycine max (L.) Merr.).

Soybean is an important oilseed cum vegetable crop, susceptible to various biotic stresses which is attributed to recent decline in crop productivity. The emergence of virulent biotypes/strains of different plant pathogens necessitates the development of new crop varieties with enhanced host resistance mechanisms. Pyramiding of multiple disease-resistant genes is one of the strategies employed to develop durable disease-resistant cultivars to the prevailing and emerging biotypes of pathogens. The present study, reports the successful introgression of two major R-genes, including Rps2 (Phytophthora rot resistance), Rmd-c (complete-powdery mildew resistance) and effective nodulating gene (rj2) through functional Marker-Assisted Backcross Breeding (MABB) in the genetic background of well-adapted and high yielding soybean varieties, CO 3 and JS 335. We have identified several promising introgressed lines with enhanced resistance to Phytophthora rot and powdery mildew. The improved soybean lines have exhibited medium to high level of resistance against powdery mildew and Phytophthora rot as well as displayed effective nodulation capacity. Our study has proven the generation of resistant genotypes to realize the potential of MABB for achieving host plant resistance in soybean. The improved lines developed can greatly assist the soybean breeding programs in India and other soybean growing countries for evolving disease-resistant varieties.

Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction.

Barnyard millet (Echinochloa species) has become one of the most important minor millet crops in Asia, showing a firm upsurge in world production. The genus Echinochloa comprises of two major species, Echinochloa esculenta and Echinochloa frumentacea, which are predominantly cultivated for human consumption and livestock feed. They are less susceptible to biotic and abiotic stresses. Barnyard millet grain is a good source of protein, carbohydrate, fiber, and, most notably, contains more micronutrients (iron and zinc) than other major cereals. Despite its nutritional and agronomic benefits, barnyard millet has remained an underutilized crop. Over the past decades, very limited attempts have been made to study the features of this crop. Hence, more concerted research efforts are required to characterize germplasm resources, identify trait-specific donors, develop mapping population, and discover QTL/gene (s). The recent release of genome and transcriptome sequences of wild and cultivated Echinochloa species, respectively has facilitated in understanding the genetic architecture and decoding the rapport between genotype and phenotype of micronutrients and agronomic traits in this crop. In this review, we highlight the importance of barnyard millet in the current scenario and discuss the up-to-date status of genetic and genomics research and the research gaps to be worked upon by suggesting directions for future research to make barnyard millet a potential crop in contributing to food and nutritional security.

Genetic enhancement of phosphorus starvation tolerance through marker assisted introgression of OsPSTOL1 gene in rice genotypes harbouring bacterial blight and blast resistance.

Phosphorus (P), an essential macronutrient, is a prerequisite for various plant-growth mechanisms including root establishment/development, early/late vegetative stage development and reproductive stage development. Rice (Oryza sativa) is very sensitive to P starvation. Most cultivated genotypes have poor tolerance levels to P deficiency and consequently the grain yield is severely affected by P starvation. Since P deficiency of soils is a major concern of rice production areas, it is necessary to develop new cultivars with enhanced P tolerance. This is also an expectation of farmers and the Agriculture ministry of southern states of India where rice cultivation is intensive. Our objective was to introgress the phosphorus starvation tolerance (OsPSTOL1) gene through marker-assisted backcross breeding (MABB) in to two intermediate genetic stocks of popular local-varieties namely, ASD 16 and ADT 43 which harbour bacterial blight and blast resistance (R) genes. To delve into the P starvation phenotypic effect, we have generated a set of four backcross inbred lines (BILs) with enhanced P starvation tolerance. The developed BILs showed altered root architecture pattern and greater root surface area with increased P uptake, confirming their adaptability to P deficient soil conditions. Further, a correlation between root traits and low/high P conditions indicates the function of introgressed OsPSTOL1 in BILs. The enhanced root characteristics, therefore, enabled the plants to access and effectively absorb available nutrients from soil. In summary, the unique features of the OsPSTOL1 BILs with bacterial blight and blast resistance can aid varietal development suitable for cultivation in P deficient soils.

Functional Marker Assisted Improvement of Stable Cytoplasmic Male Sterile Lines of Rice for Bacterial Blight Resistance.

Bacterial blight (BB), caused by Xanthomonas oryzae pv.oryzae is one among the major diseases in rice, which in severe condition cause losses up to 60% in total yield. Marker assisted pyramiding of three broad spectrum BB resistance genes (xa5, xa13, and Xa21) in prominent rice varieties is the most economical and effective strategy for the management of the BB disease. We report here the pyramiding of three genes (xa5, xa13, and Xa21) in maintainer lines (CO 2B, CO 23B, and CO 24B) of three promising wild abortive cytoplasmic male sterile lines (CO 2A, CO 23A, and CO 24A) through functional markers assisted back cross breeding. IRBB60 with xa5, xa13, and Xa21 genes is used as a donor parent. BC2F1 and BC2F2 generations from a cross of CO 2B, CO 23B, and CO 24B with IRBB60 were evaluated for bacterial blight and non-fertility restoration. In BC2F1, plants with all three resistance genes (xa5, xa13, and Xa21) and high parent genome recovery was identified. In BC2F2, plants with all resistance genes and without fertility restorer (Rf3 and Rf4) were selected. Based on agronomic traits, BB resistance and maintenance of sterility, two plants each in CO 2B × IRBB60, CO 24B × IRBB60 and one plant in CO 23B × IRBB60 combinations were identified. The identified lines were crossed with respective male sterile lines for conversion of improved B line into CMS line through back-crossing, in addition to selfing. The plants with high recurrent genome and phenotypically similar to parental lines and sterile are being used for the hybrid rice development program. Currently, using these lines (improved CMS line), test crosses were made to develop new rice hybrids. Hybrids combinations viz., CO 23A × AD08009R and CO 24A × IET20898R were found to be stable at different locations with high yield. The R line used in this study has been introgressed with xa5, xa13, and Xa21 genes in a separate breeding program. These new hybrids with resistance against bacterial blight will increase the crop production at BB environment.

TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University.

WE DEVELOPED, TNAURICE: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx.

Diversity in nucleotide binding site-leucine-rich repeat genes in cereals.

The diversity of the largest group of plant disease resistance genes, the nucleotide binding site-leucine-rich repeat (NBS-LRR) genes, was examined in cereals following polymerase chain reaction (PCR) cloning and database mining. NBS-LRR genes in rice are a large and diverse class with more than 600 genes, at least three to four times the complement of Arabidopsis. Most occur in small families containing one or a few cross-hybridizing members. Unlike in Arabidopsis and other dicots, the class of NBS-LRR genes coding for a Toll and mammalian interleukin-1 receptor (TIR) domain were not amplified during the evolution of the cereals. Genes coding for TIR domains are present in the rice genome, but have diverged from the NBS-LRR genes. Most cereal genes are similar in structure to the members of the non-TIR class of dicots, although many do not code for a coiled-coil domain in their amino termini. One unique class of cereal genes, with ~50 members, codes for proteins similar to the N-termini and NBS domains of resistance genes but does not code for LRR domains. The resistance gene repertoire of grasses has changed from that of dicots in their independent evolution since the two groups diverged. It is not clear whether this reflects a difference in downstream defense signaling pathways.