Emerging Minor Diseases of Rice in India: Losses and Management Strategies

Rice (Oryza sativa L) being one of the imperative food crops of the word contributes immensely to the food and nutritional security of India. The cultivation of rice is changed over the decades from a simple cultivation practices to the advanced cultivation to increase yield. Increased in rice yields especially after 1960s is mainly due to the introduction of high yielding semi-dwarf varieties which requires more inputs like chemical fertilizers, water and other resources. As a result, India achieved self sufficiency in rice and currently producing more than 115 MT of rice to meet country’s demand. Now India is exporting rice to other nations and earning foreign returns. With the change in rice cultivation practices, problems also aroused side by side. A number of biotic and abiotic stresses emerged as major constraints for rice cultivation in diverse agro-climatic conditions and growing ecologies. Diseases are the major biotic constraints to rice which can reduce the yields by 20–100% based on severity. Major diseases like blast, brown spot, bacterial blight, sheath blight and tungro still causing more damage and new minor diseases like bakanae, false smut, grain discoloration, early seedling blight, narrow brown spot, sheath rot have emerged as major problems. The losses due to these diseases may 1–100% based on the growing conditions, varietal susceptibility etc.., At present no significant source of resistance available for any of the above emerging diseases. But looking into the severity of these diseases, it is very important to address them by following integrated management practices like cultural, mechanical, biological and finally chemical control. But more emphasis has to be given to screen gerrmplasm against these diseases and identify stable source of resistance. Finally utilizing these sources in resistance breeding program by employing molecular breeding tools like marker assisted selection (MAS), marker assisted back cross breeding (MABB), gene pyramiding and transgenic tools. The present chapter discusses the importance of these emerging minor diseases of rice, the losses and possible management measures including resistance breeding.

New genomic regions for resistance to anthracnose (Colletotrichum lindemuthianum) through GBS-based genome-wide association study in common bean (Phaseolus vulgaris)

The most effective strategy to manage bean anthracnose (ANT), caused by Colletotrichum lindemuthianum, is the use of resistant cultivars. This study aimed to evaluate resistance reactions of common bean accessions to C. lindemuthianum races 2, 9 and 1545, and to perform genome-wide association study (GWAS). Hence, 89 accessions were phenotyped and genotyped through genotyping by sequencing (GBS). As a result, 48 accessions resistant to all evaluated races were identified. Moreover, single-nucleotide polymorphisms (SNP) significantly associated with resistance were identified in new regions of chromosomes Pv03, Pv05 and Pv06, and also at the beginning of Pv04 and end of Pv11, where other resistance genes have been previously found. In reference genome these regions contain model genes encoding resistance proteins as kinases, leucine-rich repeats, receptor-like protein, copper transport protein, pentatricopeptide repeats, calcium-dependent protein kinases, and ethylene-responsive transcription factors. The genomic regions associated to ANT resistance found in this study should be validated for further use in marker assisted selection and gene pyramiding. Together with new sources of ANT resistance our findings show promise for further crop improvement.

Genetics and Genomics of Fusarium Wilt of Chilies: A Review

Hot pepper (Capsicum annum L.) is a major spice crop and is used worldwide for its nutritional value. In the field, its plant is susceptible to various fungal diseases, including fusarium wilt, caused by soil-borne fungus Fusarium oxysporum f. sp. capsici, which can survive in the soil for several years. The infected plant can be recognized by the yellowing of older leaves and downward curling of apical shoots, followed by plant wilting and ultimately the death of the plant. The resistance mechanism in plants is controlled by a single dominant gene, and conventional plant breeding techniques are used to develop a wilt-resistant germplasm. Non-conventional techniques such as gene pyramiding and expression enhancement of antifungal genes could be used to shorten the time to develop resistance against fusarium wilt in hot peppers. In this review, we discuss different aspects of the disease and the molecular basis of resistance in chili/hot pepper plants. Furthermore, this review covers the scope of conventional and non-conventional breeding strategies and different management approaches used to tackle the disease.

Recent Advances in Rice Varietal Development for Durable Resistance to Biotic and Abiotic Stresses through Marker-Assisted Gene Pyramiding

Abiotic and biotic stresses adversely affect rice growth, development and grain yield. Traditional rice breeding techniques are insufficient in modern agriculture to meet the growing population’s food needs on a long-term basis. The development of DNA markers closely linked to target genes or QTLs on rice chromosomes, and advanced molecular techniques, such as marker-assisted selection (MAS), have encouraged the evolution of contemporary techniques in rice genetics and breeding, such as gene pyramiding. Gene pyramiding refers to the act of combining two or more genes from multiple parents into a single genotype, which allows the overexpression of more than one gene for broad-spectrum abiotic and biotic stress resistance. Marker-assisted pedigree, backcrossing and pseudo-backcrossing methods can increase the conventional breeding speed by reducing the number of breeding generations in order to enhance the pyramiding process. Pyramiding is affected by several factors: the number of transferred genes; the range within gene and flanking markers; the number of chosen populations in every breeding generation; the features of genes and germplasms; and the potentiality of breeders to identify the target genes. Modern breeding methods, such as the marker-assisted backcrossing approach, have made gene pyramiding more precise and reliable for the development of stress-tolerant rice varieties in the coming decades. This review presents up-to-date knowledge on gene pyramiding schemes, marker-assisted gene pyramiding techniques, the efficiency of marker-assisted gene pyramiding and the advantages and limitations of gene pyramiding methods. This review also reports on the potential application of marker-assisted selection breeding to develop stress-tolerant rice varieties that stabilize abiotic and biotic stresses. This review will help rice breeders to improve yields by increasing rice productivity under abiotic and biotic stress conditions.

Wheat Responses, Defence Mechanisms and Tolerance to Drought Stress: A Review Article

Wheat (Triticum aestivum L.) is one of the major basic stable crops grown worldwide, however, it is sensitive to environmental stresses like drought. With climate change, drought stress is becoming an increasingly severe constraint on wheat production which affects the plant growth and development, physiological functions, grain formation, grain quality and ultimately the yield. Various responses including biochemical, physiological, morphological, and molecular adaptations are shown by plants to survive in the drought stress condition. Drought escape, avoidance and tolerance are important coping mechanisms of wheat plant under drought environment. Several mechanisms such as accumulation of ABA, osmotic adjustment, and induction of dehydrins may confer drought tolerance by maintaining the high tissue water potential. As the root structure and root biomass define the pattern of water extraction from the soil, enhanced root and suppressed shoot growth resulting in higher root: shoot ratio facilitated plants to drought tolerance. The development of drought tolerance varieties becomes an important due to the uneven distribution of rainfall and water shortage. Some growth stage-specific physio-morphological traits are fundamental targets to breed drought-tolerant wheat varieties. Mutation breeding, molecular breeding, genome engineering techniques including gene pyramiding, gene stacking, and transgenics are employed to breed wheat for tolerance to abiotic stresses including drought. Omics decode the entire genome to have better understanding of plant molecular responses that will provide precise strategies for crop improvement. This paper discusses the wheat plant’s responses to drought stress, their defense mechanisms and modern techniques for the development of drought tolerant wheat varieties.

Identification of Root Rot Resistance QTLs in Pea Using Fusarium solani f. sp. pisi-Responsive Differentially Expressed Genes

Pisum sativum (pea) yields in the United States have declined significantly over the last decades, predominantly due to susceptibility to root rot diseases. One of the main causal agents of root rot is the fungus Fusarium solani f. sp. pisi (Fsp), leading to yield losses ranging from 15 to 60%. Determining and subsequently incorporating the genetic basis for resistance in new cultivars offers one of the best solutions to control this pathogen; however, no green-seeded pea cultivars with complete resistance to Fsp have been identified. To date, only partial levels of resistance to Fsp has been identified among pea genotypes. SNPs mined from Fsp-responsive differentially expressed genes (DEGs) identified in a preceding study were utilized to identify QTLs associated with Fsp resistance using composite interval mapping in two recombinant inbred line (RIL) populations segregating for partial root rot resistance. A total of 769 DEGs with single nucleotide polymorphisms (SNPs) were identified, and the putative SNPs were evaluated for being polymorphic across four partially resistant and four susceptible P. sativum genotypes. The SNPs with validated polymorphisms were used to screen two RIL populations using two phenotypic criteria: root disease severity and plant height. One QTL, WB.Fsp-Ps 5.1 that mapped to chromosome 5 explained 14.8% of the variance with a confidence interval of 10.4 cM. The other four QTLs located on chromosomes 2, 3, and 5, explained 5.3–8.1% of the variance. The use of SNPs derived from Fsp-responsive DEGs for QTL mapping proved to be an efficient way to identify molecular markers associated with Fsp resistance in pea. These QTLs are potential candidates for marker-assisted selection and gene pyramiding to obtain high levels of partial resistance in pea cultivars to combat root rot caused by Fsp.

The Impact of Climate Change on the Resistance of Rice Near-Isogenic Lines with Resistance Genes Against Brown Planthopper

Background The impact of climate change on insect resistance genes is elusive. Hence, we investigated the responses of rice near-isogenic lines (NILs) that carry resistance genes against brown planthopper (BPH) under different environmental conditions. Results We tested these NILs under three environmental settings (the atmospheric temperature with corresponding carbon dioxide at the ambient, year 2050 and year 2100) based on the Intergovernmental Panel on Climate Change prediction. Comparing between different environments, two of nine NILs that carried a single BPH-resistant gene maintained their resistance under the environmental changes, whereas two of three NILs showed gene pyramiding with two maintained BPH resistance genes despite the environmental changes. In addition, two NILs (NIL-BPH17 and NIL-BPH20) were examined in their antibiosis and antixenosis effects under these environmental changes. BPH showed different responses to these two NILs, where the inhibitory effect of NIL-BPH17 on the BPH growth and development was unaffected, while NIL-BPH20 may have lost its resistance during the environmental changes. Conclusion Our results indicate that BPH resistance genes could be affected by climate change. NIL-BPH17 has a strong inhibitory effect on BPH feeding on phloem and would be unaffected by environmental changes, while NIL-BPH20 would lose its ability during the environmental changes.

Rice Blast Disease in India: Present Status and Future Challenges

Rice (Oryza sativa L.) is the staple food of the majority of Indians, and India is both the major producer and consumer of rice. Rice cultivation in India is confronted with diverse agro-climatic conditions, varying soil types, and several biotic and abiotic constraints. Among major fungal diseases of Rice in India, the blast caused by Magnaporthe oryzae is the most devastating disease, with the neck blast being the most destructive form. Most of the blast epidemic areas in India have been identified with a mixture of races blast fungus resulting in the resistance breakdown in a short period. At present, a more significant number of the rice varieties cultivated in India were bred by conventional breeding methods with blast resistance conferred by a single resistance gene. Therefore, the blast disease in India is predominantly addressed by the use of ecologically toxic fungicides. In line with the rest of the world, the Indian scientific community has proven its role by identifying several blast resistance genes and successfully pyramiding multiple blast resistance genes. Despite the wealth of information on resistance genes and the availability of biotechnology tools, not a great number of rice varieties in India harbor multiple resistance genes. In the recent past, a shift in the management of blast disease in India has been witnessed with a greater focus on basic research and modern breeding tools such as marker-assisted selection, marker-assisted backcross breeding, and gene pyramiding.

Gene stacking: Approach of genetic engineering

Gene stacking is the process of addition of two or more gene of interest into a single plant. The combination or stacking of different traits or genes in plants is rapidly gaining popularity in biotech crop production. The new evolved trait is known as stacked trait and the crop is known as biotech stacked or simply stacked. This can be accomplished in many ways, one of which is gene pyramiding. Biotech stacks give crops a larger genetic and agronomic boost, allowing them to perform better in challenging farming situations. Biotech stacks are designed to increase productivity by overcoming biotic and abiotic challenges like as insect pests, diseases, weeds, and environmental stress. This review will explain about the gene stacking principle, the need for biotech stacking, and the many gene stacking methods.