The dominance of salt water across the surface of the earth has lead to the widespread occurrence of salt-affected soils. Salt-tolerant plants (halophytes) have evolved to grow on these soils, with halophytes and less tolerant plants showing a wide range of adaptations. However, most of our crops are salt-sensitive. Consequently, salinity is an ever-present threat to agriculture, especially in areas where secondary salinisation has developed through irrigation or deforestation. Attempts to improve the salt tolerance of crops have met with very limited success, due to the complexity of the trait, both genetically and physiologically. Tolerance shows all the characteristics of a multigenic trait, with quantitative trait loci (QTLs) identified in barley, citrus, rice and tomato. Attempts to produce salt-tolerant crops have involved both the domestication of halophytes and the manipulation of existing crop species through conventional breeding programmes, the use of in vitro selection, pooling physiological traits, interspecific hybridisation, the use of marker-aided selection and the development of transgenic plants. After 10 years of research, the value of using transgenic plants to alter salt tolerance has yet to be tested in the field. The use of physiological traits in breeding programmes and the domestication of halophytes currently offer viable alternatives to the development of tolerance through the use of transgenic technologies.

Why does salinity pose such a difficult problem for plant breeders

Empirical threshold values for quantitative trait mapping.

There is a need to integrate conceptual framework based on the current understanding of salt stress responses with different approaches for manipulating and improving salt tolerance in crop plants. Soil salinity exerts significant constraints on global crop production, posing a serious challenge for plant breeders and biotechnologists. The classical transgenic approach for enhancing salinity tolerance in plants revolves by boosting endogenous defence mechanisms, often via a single-gene approach, and usually involves the enhanced synthesis of compatible osmolytes, antioxidants, polyamines, maintenance of hormone homeostasis, modification of transporters and/or regulatory proteins, including transcription factors and alternative splicing events. Occasionally, genetic manipulation of regulatory proteins or phytohormone levels confers salinity tolerance, but all these may cause undesired reduction in plant growth and/or yields. In this review, we present and evaluate novel and cutting-edge approaches for engineering salt tolerance in crop plants. First, we cover recent findings regarding the importance of regulatory proteins and transporters, and how they can be used to enhance salt tolerance in crop plants. We also evaluate the importance of halobiomes as a reservoir of genes that can be used for engineering salt tolerance in glycophytic crops. Additionally, the role of microRNAs as critical post-transcriptional regulators in plant adaptive responses to salt stress is reviewed and their use for engineering salt-tolerant crop plants is critically assessed. The potentials of alternative splicing mechanisms and targeted gene-editing technologies in understanding plant salt stress responses and developing salt-tolerant crop plants are also discussed.

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Engineering salinity tolerance in plants: progress and prospects.

Soil salinization and a degraded ecological environment are challenging agricultural productivity and food security. Rice (Oryza sativa), the staple food of much of the world's population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. Salt tolerance is a complex quantitative trait. Biotechnological efforts to improve the salt tolerance of rice hinge on a detailed understanding of the molecular mechanisms underlying salt stress tolerance. In this review, we summarize progress in the breeding of salt-tolerant rice and in the mapping and cloning of genes and quantitative trait loci (QTLs) associated with salt tolerance in rice. Furthermore, we describe biotechnological tools that can be used to cultivate salt-tolerant rice, providing a reference for efforts aimed at rapidly and precisely cultivating salt-tolerance rice varieties.

https://www.mdpi.com/1422-0067/21/21/8385/pdf

Advances and Challenges in the Breeding of Salt-Tolerant Rice.

espanolLa seleccion para resistencia a la salinidad de genotipos de arroz, basada solamente en el comportamiento fenotipico, es menos confiable y retarda el avance en el mejoramiento. Se han utilizado avances recientes en marcadores moleculares, microsatelites o repeticiones de secuencias simples (SSR por sus siglas en ingles) para determinar genotipos de arroz tolerantes a la salinidad. Se utilizaron tres marcadores SSR viz., RM7075, RM336 y RM253 para evaluar genotipos de arroz para tolerancia a la salinidad. La evaluacion fenotipica y genotipica para la tolerancia a la salinidad se realizo en la etapa de plantula. La fenotipificacion de once genotipos se realizo en un sistema hidroponico utilizando solucion nutritiva salinizada (CE 12 dS/m). Se siguio el protocolo estandarizado del IRRI para evaluar la tolerancia a la salinidad. Se detecto una gran variacion en la tolerancia a la salinidad entre el germoplasma de arroz. La altura de las plantulas y la materia seca total de las lineas tolerantes se redujeron en un 19,0 y 40,6%, respectivamente, bajo estres salino (CE 12 dS/m), en tanto que las de las lineas susceptibles se redujeron en un 46,0% y 73,5%, respectivamente. Los marcadores mostraron polimorfismo y fueron capaces de discriminar los genotipos tolerantes a la salinidad de aquellos susceptibles. Los genotipos con un patron similar de bandas a Pokkali se consideraron como tolerantes a la salinidad. Los marcadores SSR (RM7075, RM336 y RM253) identificaron ocho, nueve y siete genotipos tolerantes a la salinidad, respectivamente. A traves del estudio fenotipico y genotipico, tres genotipos viz., Pokkali, TNDB-100 y THDB se identificaron como cultivares de arroz tolerantes a la salinidad. Estos marcadores SSR podrian tener homologia de secuencias con genotipos de arroz tolerantes a la salinidad y por consiguiente, los marcadores podrian ser capaces de identificar genotipos de arroz tolerantes a la salinidad de aquellos susceptibles. EnglishSelection for salinity tolerant genotypes of rice based on phenotypic performance alone is less reliable and will delay in progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs), have been useful in finding salt tolerant rice genotypes. Three selected SSR markers already known to be polymorphic, viz., RM7075, RM336 and RM253, were used to evaluate rice genotypes for salt tolerance. Phenotypic and genotypic evaluation for salinity tolerance was done at the seedling stage. Phenotyping was done in hydroponic system using salinized (EC 12 dS/m) nutrient solution following IRRI standard protocol. Large variation in salinity tolerance among the rice germplasms was detected. Salt stress (EC 12 dS/m) reduced seedling height by 19.0% and total dry matter of tolerant lines by 40.6%, whereas, total dry matter of susceptible lines were reduced by 46.0-73.5%. All the tested markers were polymorphic and were able to discriminate salt tolerant genotypes from susceptible. The genotypes having similar banding pattern with Pokkali were considered as salt tolerant. Markers RM7075, RM336 and RM253 identified eight, nine and seven salt tolerant genotypes, respectively. Through phenotypic and genotypic study, three genotypes viz., Pokkali, TNDB-100 and THDB were identified as salt tolerant rice genotypes. These SSR markers might have sequence homology with salt tolerant rice genotypes and consequently the markers could able to identify salt tolerant rice genotypes from susceptible ones

Phenotypic and genotypic screening of rice genotypes at seedling stage for salt tolerance.

Salinity is the second most important abiotic stress after drought that hampers rice production, especially in south and Southeast Asia. Breeding approach supplemented with molecularmarkers-assisted selection is the most promising approach in terms of efficiency to increase the productivity under salt-affected soils. Thirty-day-old rice seedlings of 300 F5:6 recombinant-inbred lines derived from a cross between the salt sensitive, IR29 (indica), and a salt tolerant, Hasawi (aus), were used to identify quantitative trait loci (QTLs) linked to salinity tolerance. One hundred and ninety four polymorphic SNP markers were used to construct a genetic linkage map involving 142 selected RILs that covered 1441.96 cM genome with an average distance of 7.88 cMbetween loci. Twenty new QTLs (LOD > 3) were identified on chromosomes 1, 2, 4, 6, 8, 9 and 12 using composite interval mapping with R2 as high as >20% with LODvalue of 7.21. Many earlier studies reported big qSaltol for seedling stage salinity tolerance in rice is on short arm of chromosome 1 but none of the QTL in our study was on qSaltol or nearby position, therefore, Hasawi conferred salinity tolerance in RILs due to novel QTLs. It is suggested to fine map the novel QTLs so that the level of salinity tolerance could be further enhanced by pyramiding of the different QTLs in one genetic background through marker-assisted selection.

A. Luzi-Kihupi

Papers

Identification of quantitative trait loci for salinity tolerance in rice (Oryza sativa L.) using IR29/Hasawi mapping population.