Search

Association mapping approach was applied to identify regions linked to SSR markers with yield and related traits in drought stress conditions using 267 autumn rice germplasm collection of Assam. The germplasm exhibited extensive phenotypic and genotypic diversity in both irrigated and artificial drought stress conditions. The drought screening in rainout shelter was successful causing a reduction of mean yield up to 65% in contrast to irrigated conditions. The grain yield showed a positive correlation with traits like productive tiller number, spikelet fertility, and relative leaf water content in drought stress situations suggesting their scope for use as an indirect selection parameter in breeding autumn rice. Many traditional autumn genotypes like ‘Koni ahu’, ‘Garam ahu 2’, ‘Bengonagutiya’, ‘Ahu Joha’ were found to be tolerant in drought stress conditions. The population structure study revealed the presence of structure in the panel dividing 203 accessions into two subgroups and leaving sixty-nine accessions under admixed ancestry. The marker-trait association (MTA) studies using structured mixed linear model (MLM) method unveiled 64 MTA for nine different traits under drought stress conditions. For grain yield, six MTA’s were reported on chromosome 2, 3, 5, 6 and 10 explaining the Phenotypic Variance in the range of 6 to 16%. Seven novel MTA were obtained for their corresponding traits and many of the identified QTL’s were reported previously. Some of the associations were also consistent with General linear model study. Candidate gene analysis of associated marker regions inferred that there are certain stress-responsive genes in its proximity. The tolerant genotypes identified can be employed in different drought breeding programs. The novel associations with major effect offer scope in the mining of new alleles for traits associated with drought tolerance for this class of rice.

Undesirable environmental situations, namely, drought, extreme salinity, and temperature, are the most common abiotic stresses constantly challenge in various agricultural regions. These types of stress(s) ultimately result in yield loss to different crop species. Under the influence of abiotic stresses, most horticultural crop species (tomato, banana, soybean, etc.) induce activation of genes for stress physiology. Boosting up the level of heat shock proteins (HSPs)/chaperones in a diverse range of stresses signifies its importance in metabolic stress response. In plants it belonges to divergent classes and are homologous to prokaryotes and other eukaryotes. Chaperones are the essential mechanism under adverse conditions to maintain homeostasis at the cellular level. Interaction of molecular chaperones with misfolded or newly synthesized proteins assists proper folding of proteins. However, molecular chaperones like protein disulfide isomerase, cyclophilin, and calnexin/calreticulin, have also been found to activate defence response against abiotic stresses in various crop species. This activity specifies the importance of HSPs as stress-responsive cascade and therefore, considering its vital role in genome-wide studies in several crop species. The chaperone network's sensitive tuning and its reciprocal relationship with other cellular components are still yet to be researched to know the appropriate character and function of chaperones. In the present chapter, the emphasis has been given to describe the structure and characteristics of diverse HSP and plant-cell chaperones in the endoplasmic reticulum of various horticulture crops. We also describe the mechanism of molecular chaperon under adverse climatic conditions and during the accumulation of seed storage protein at the development phase of seeds.

With the advancement in transcriptomic technology, it is now possible to get insights into undescribed phenomena of the continually evolving arms race of plant–pathogen interactions. The study of this interaction describes various mechanisms such as the plant defense pathway, regulatory gene annotation, gene network, and biochemical metabolism of plants and pathogens, which still remain a major challenge in agriculture. Researchers can understand the mechanisms of altering gene expression during compatible and incompatible interaction of pathogenic organisms at the molecular level. Transcriptome profiling could efficiently identify the differential changes in gene expression in response to infection, and thereby provide information regarding the basal defense system, resistance, pathogenicity of plant pathogens, and the difference between host and nonhost defense mechanisms of plants. Based on this information, several broad spectrum disease-resistant crop plants have been generated.

Due to global warming, low water stress (drought) becomes a critical abiotic factor that adversely affect yield up to 50% in major horticultural crops. An insight into morpho-anatomical, physiological, and biochemical changes in drought-affected crops provides vital information to design the best strategy for reducing the influence of drought on horticultural crops. These strategies are determined by the capacity to enhance the root–nutrient relationship by reducing the deficit of soil moisture, lowering the drought impact, and accelerating the recovery process. Remedies and management strategies are being followed to cope with drought stress such as mulching, efficient irrigation, proper nutrient supply, application of plant growth–promoting rhizobacteria, and selection of climate-resilient varieties. The improvement in technologies paved the way for augmentation of drought-related genomics and transcriptomics studies, which further strengthens the quantitative trait loci mapping, genome-wide association studies, and genomic-selection strategies. Current drought stress–management technologies are based on the application of transgenic technology along with genome-editing tools for genetic modification of horticulture crops. The advancement in modern omics tools like genomics, proteomics, phenomics, and metabolomics has also enhanced the improvement of horticulture crops. Furthermore, these technologies have created new opportunities for the develop novel mitigation strategies for drought-prone horticultural crops. In the present chapter, we mainly focus on modern approaches in horticultural crops to mitigate the adverse effects of drought.

Leaf, stem and stripe rust diseases seriously threaten wheat production worldwide. The obligate biotrophic rust pathogens are highly capable of producing new virulent races that can overcome resistance. To defy the emerging threat of rusts in wheat, attempts are going on at global level for identification of pathotypes, new sources of resistance and deployment of resistant varieties for management of these rusts. Several rust resistance genes (>200) and their associated molecular markers are available to breeders for their use in rust resistance breeding programme. Molecular markers have been extensively used in wheat breeding programmes for various reasons, of which linkage and QTL map being on the top list. Linkage maps depict the presence of major genes and QTLs on chromosomal regions. Molecular markers associated with many effective resistance genes are now increasingly available and have been successfully utilized in many wheat breeding programmes. Marker systems like SSR, STS, SCAR, DArT and SNPs are now popularly being used because of their robustness. MAS and more traditional screening methods like seedling resistance test (SRT) against the rust pathotypes are often complementary, and both are utilized depending on the generation. MAS has important application when two or more resistance genes against particular rust need to be pyramided in a single wheat genotype. In such cases where screening with the pathotypes is not able to confirm the presence of two or more resistance genes conferring resistance against all the pathotypes of the disease, MAS helps in the selection. The various approaches presently being used for MAS has been discussed in this chapter along with the successful examples of mapping various rust resistance genes and their introgression into elite wheat cultivars using various marker-assisted breeding strategies.

Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] commonly known as kulthi or Madras gram is an important drought tolerant legume crop used as food and fodder in India and across the globe. Horsegram is tolerant to many biotic and abiotic stresses and considered a potential future food legume. Despite being a multiutility crop, insufficient genomic information is available in this species, which is otherwise required for genetic improvement. Hence, in the present work we used next-generation sequencing (NGS) technology for genome-wide development and characterization of novel simple sequence repeat (SSR) markers in horsegram. In all, 2458 SSR primer pairs were designed from NGS data and 117 SSRs were characterized in 48 diverse lines of horsegram. Cross-transferability of these markers was also checked in nine related legume species. The polymorphic SSRs revealed high diversity measures such as mean values of expected heterozygosity (He; 0.54), observed heterozygosity (Ho; 0.64), and polymorphism information content (PIC; 0.46). Analysis of molecular variance (AMOVA) revealed high degree of genetic variance within the populations. Dendrogram based on Jaccard’s similarity coefficient and principal component analysis (PCA) revealed two groups in the analyzed accessions. This observation was further confirmed by Bayesian genetic STRUCTURE analysis. The SSR markers developed herein can be used in diverse genetic analysis including association mapping in this crop and also in related legume crops with limited marker resources. Hence, this new SSR dataset can be useful for molecular breeding research in this underutilized pulse crop. In addition, genetic diversity estimates of analyzed germplasm can be important for devising future breeding programmes in horsegram.