Harmonizing technological advances in phenomics and genomics for enhanced salt tolerance in rice from a practical perspective

Abstract

Half of the global human population is dependent on rice as a staple food crop and more than 25% increase in rice productivity is required to feed the global population by 2030. With increase in irrigation, global warming and rising sea level, rising salinity has become one of the major challenges to enhance the rice productivity. Since the loss on this account is to the tune of US$12 billion per annum, it necessitates the global attention. In the era of technological advancement, substantial progress has been made on phenomics and genomics data generation but reaping benefit of this in rice salinity variety development in terms of cost, time and precision requires their harmonization. There is hardly any comprehensive holistic review for such combined approach. Present review describes classical salinity phenotyping approaches having morphological, physiological and biochemical components. It also gives a detailed account of invasive and non-invasive approaches of phenomic data generation and utilization. Classical work of rice salinity QLTs mapping in the form of chromosomal atlas has been updated. This review describes how QTLs can be further dissected into QTN by GWAS and transcriptomic approaches. Opportunities and progress made by transgenic, genome editing, metagenomics approaches in combating rice salinity problems are discussed. Major aim of this review is to provide a comprehensive over-view of hitherto progress made in rice salinity tolerance research which is required to understand bridging of phenotype based breeding with molecular breeding. This review is expected to assist rice breeders in their endeavours by fetching greater harmonization of technological advances in phenomics and genomics for better pragmatic approach having practical perspective.

Identification of QTLs Controlling Salt Tolerance in Cucumber (Cucumis sativus L.) Seedlings

“…In recent years, many QTLs related to the salt tolerance of major field crops such as rice, soybean, wheat, and maize, as well as vegetable crops such as cabbage and tomato have been reported [ 13 , 14 , 20 , 21 , 22 , 23 ]. But currently there are few reports on the mining of cucumber salt tolerant genes, and no QTL mapping studies have been carried out.…”

Advances and Challenges in the Breeding of Salt-Tolerant Rice

“…The development of an efficient and reliable evaluation system is a prerequisite for breeding salt-tolerant rice varieties. The current rice salt tolerance indicators are divided into two aspects: morphological parameters and physiological parameters [18,19]. The morphological parameters evaluation method is to conduct salt treatments at different growth stages of rice and then observe and record the salt damage symptoms of plants, leaves, tillers, and spikelet fertility [20,21].…”

“…The evaluation of rice salt tolerance is also complex. Phenotypic traits are typically used to evaluate the salt tolerance of rice varieties [18], an approach that lacks comprehensiveness and accuracy and may result in an assessment of salt tolerance that is not consistent with actual performances in the field. Therefore, a standardized system to evaluate rice salt tolerance is urgently needed.…”

Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

“…Compared to the comprehensive soil control and optimized regionalization of farming, the most cost-efficient strategy for coping with the stress is breeding and utilizing high saline and alkali tolerant cultivars [ 15 , 16 ]. Hence understanding the inheritance and genetics of the saline and alkali tolerances is a prerequisite of modern breeding practices [ 17 ].…”