Genotypic and phenotypic characterization of ‘Saltol’ introgression lines for release as high yielding salt tolerant rice

Abstract

Rice is the staple food for more than 160 million people of Bangladesh. It is not just a cereal but the daily necessity for most of the people in the country. Rice is the synonym of food in Bangladesh since it provides about 72%, 62% and 17% of the calorie, protein and fat requirement of the population, respectively. Therefore, food security in Bangladesh may be regarded as rice security in the country. The country was at the brim of food security recently after attaining self-sufficiency in rice. But the sustainability of this sufficiency is encountering a lot of challenges like population growth, decreasing land, technological limitation, resource limitation, abuse of technologies, environmental pollution, climatic adversities, etc. However, among the different challenges, soil salinity is a serious environmental stress after submergence and drought which is threatening the rice productivity and food security of Bangladesh. Salinity intrusion has been increasing slowly but continuously. In the past four decades (1973 to 2012) it has been increased to more than 26% and the total affected area is now approaching >1.06 Mha. Rice is most sensitive to salinity but suited for growth the saline marshy land of the saline coastal belt in Bangladesh. The higher sensitivity of modern varieties to saline stress forces farmers to continue growing their traditional landraces, which however have low yields. Therefore, development of salt tolerant modern rice has been considered one of the feasible strategies to increase the total rice production of the country and maintain the sustainability of self-sufficiency. Salinity tolerance of rice is a complex trait affected by various genetic and non-genetic factors, and its improvement via conventional breeding has been slow. Recent advancements of molecular breeding have led to the development of more efficient selection tools like molecular marker based selection to substitute phenotype based selection systems. The success of molecular breeding approach like marker-assisted backcrossing (MABC) has been demonstrated by the introgression of Sub1, a major QTL for submergence tolerance into several mega varieties. Therefore, a major QTL associated with the Na+/K+ratio and seedling-stage salinity tolerance, named Saltol, was targeted to improve seedling stage salinity tolerance of two Bangladeshi mega rice variety BR11 (for transplated aman season) and BRRI dhan28 (for boro season) through MABC approach. Three-backcross generation MABC approach was used to introgress the Saltol QTL through SSR and InDel markers. Single Nucleotide Polymorphism (SNP) markers were also used to further check any potential background donor introgression of the selected lines from both MABC events. To study the phenotypic gain due to Saltol QTL in to the background of BR11 and BRRI dhan28, a number of studies were carried out with the developed lines at seedling and reproductive stages in controlled net house condition as well as in saline and non-saline field conditions respectively. Three backcrosses and two selfing generations were carried out to transfer the positive alleles of Saltol QTL from FL378, a F8 RIL developed from IR29/Pokkali. From first MABC event (BR11-Saltol), two Near Isogenic Line (NIL), NIL52 and NIL1 were selected at BC3F3 stage with 1.3 million bases/mega bases (Mb) introgression at the Saltol region (donor genome percentage is 3.33%) and about 96.67% of BR11 genome at the background. At later generations, 4 lines from NIL52 and 8 lines from NIL1 were selected phenotypically based on grain size for obtaining further homogeneity. To optimize the effect of Saltol, a different strategy was applied by increasing the size of the introgressed segment at the target Saltol region for the second MABC event (BRRI dhan28-Saltol). Four different size donor segments at the Saltol i.e. 1.3 Mb (2.73%), 2.4 Mb (3.64%), 3.3 Mb (4.55%) and 3.7 Mb (5.45%) were introgressed in to BRRI dhan28 background. Eleven NILs (NIL188, NIL204, NIL318, NIL341, NIL412, NIL434, NIL448, NIL607, NIL657, NIL683 and NIL807) at BC3F3 stage were selected with 91.82-95.45% recovery of the BRRI dhan28 genome. SNP assay identified single SNP (id1008684 at 12869918 bp) for 1.3 Mb and 2 SNP (id1008684 at 12869918 bp and id1009616 at 14592566 bp) for the larger segments i.e. 3.3-3.7 Mb at the Saltol region. For further checking background donor introgression through SNP markers, a number of background introgressions were detected for both BR11-Saltol NILs, having ~94% and ~80% recovery of BR11 genomes for NIL52 and NIL1 respectively. For BRRI dhan28-Saltol the recovery was better with respect to SSR and InDel markers for all NILs and the recovery ranged from 97% to 88%. The phenotypic gain for the first MABC event with a maximum reduction of seedling shoot Na+/K+ ratio by about 20% due to 1.3 Mb donor segment at the target Saltol loci into BR11. While the second MABC event the utmost reduction is about 32% by introgressing large donor segment (3.3 Mb) at the target Saltol loci in case of BRRI dhan28 for seedling stage salinity tolerance. Apparently, large introgression 3.7 Mb at the Saltol loci improves the overall salinity tolerance in terms of SES. A total of 13 lines/NILs (7 BR11-Saltol i.e. BR11- 52-124, BR11-52-55, BR11-52-145, BR11-52-67, BR11-150, BR11-65, BR11-7 and 6 BRRI dhan28-Saltol i.e. NIL434, NIL412, NIL607, NIL618, NIL657, NIL683) were finally selected based on tolerance at seedling stage and for yield at field conditions. All agronomic and grain quality parameters for most of the developed lines/NILs from both MABC events showed successful recovery of the BR11 and BRRI dhan28 traits with an improvement of yield potential in both saline and non-saline field conditions. NIL52 of BR11-Saltol and NIL434, NIL657, NIL683 of BRRI dhan28-Saltol performed better in a moderate salinity stress (6-8 dSm-1) condition during reproductive stage in controlled Net house condition. Genotype by environment interaction analyses of four-environment trials of BR11-Saltol lines showed a significant G by E interactions identified by AMMI-2 model. Stability analyses identified 3 BR11-Saltol lines such as BR11-52-124, BR11-52-67 and BR11-7 with superior performance in better environments. Therefore these could be suited for cultivation in better environments, whereas a line BR11-65 could be recommended for cultivation all over the country due to its stable and average performances across different environment. On the other hand, 3 NILs (NIL434, NIL607 and NIL683) of BRRI dhan28-Saltol showed better yields compared to the recipient while evaluated in saline and non-saline environments and could be recommended for further evaluation. Salinity tolerance is a complex phenomenon, and several complementary biochemical and physiological adaptations are generally necessary to establish complete tolerance. The Saltol locus is just one component of a multifaceted strategy to improve rice yields on salt affected soils. The initial steps have been taken to use the MABC transfer of Saltol alleles into popular varieties to test the efficacy of this allele to provide seedling stage tolerance. Pyramiding of QTLs with complementary physiological and biochemical mechanisms could be the next step to forward further for getting higher and durable tolerances including the tolerance for the whole growth period.