Salt stress (both salinity and alkalinity/sodicity) is a worsening problem in inland areas in sub-Saharan Africa such as in Mali, Ethiopia, and Burundi because of the buildup of salt as a consequence of the excessive use of irrigation water with improper drainage, coupled with the use of poor-quality irrigation water or sodic soils developed from salt-bearing rocks. Over 20 million hectares of land suited to rice production in Asia are currently either underexploited or unexploited because of excess salt and other related soil problems, and in India and Bangladesh alone, productivity of more than 7 million hectares of rice land is adversely affected by salt stress. Salt-affected areas are predominantly inhabited by impoverished communities with fewer opportunities for food security and livelihood options.

Damaged rice variety, BRRI dhan 28, due to excessive salt in field


Gene discovery and MAS

Phenotyping capacity for early seedling stage salt tolerance has been enhanced at the AfricaRice Irrigated Lowland Breeding Unit in Senegal to more than 5,000 lines per year. Rapid and reliable evaluation of landraces for tolerance to salinity at the seedling stage was conducted at Mbe, Cote d'Ivoire using high-throughput phenotyping facilities. SSR and SNP analyses were done to confirm differences in alleles controlling tolerance in new donors and that of Saltol. The Phenomics of Rice Adaptation and Yield (PRAY) indica panel of 300 accessions screened at Ndiaye, Senegal for seedling and reproductive stage salt tolerance under field conditions at 4 dSm-1, and 60% of these accessions had a yield of <1.0 tons/ha. However, the top 5% of the accessions (14 entries) had yields of >3.0 tons/ha (3.06 - 4.7 tons/ha). Separately, three different mapping populations using new salt tolerance donors (Sahel 317 x Madina koyo, Sahel 329 x Madina Koyo, and Sahel 329 x NERICA-L-9) were phenotyped in three sites (Senegal, Cote d'Ivoire, and Serra Leone) at both vegetative and reproductive stages. Allele discovery work is ongoing using DArT seq with >50k SNPs. Ninety-six (94) salt-tolerant lines

from the IRRI HQ sourced from IRRI (30 lines), Philippines (23 lines), Bangladesh (3 lines), Myanmar (4 lines), Vietnam (1 line), India (3 lines), and Mozambique (30 lines), as well as five from Kenya as local checks were screened in Hola/Bura, from which 18 salt-tolerant lines were selected. Thirty-five (35) multi-QTL marker-assisted introgression lines (Saltol, Sub1 and AG) were received from IRRI and evaluated in both Senegal and Cote d'Ivoire, of which 14 lines have been selected for advancement. QTL discovery for salt tolerance is ongoing as part of a PhD thesis in collaboration with KAUST University in Saudi Arabia.

Large-scale control facility

The project established a semi-high-throughput facility for screening for seedling stage salinity tolerance in 2016 where 18,374 different genotypes/landraces from Sri Lanka, Indonesia, Myanmar, and India including the 3K rice genome panel were evaluated. A total of 112 accessions were found tolerant under EC 12 and EC 18 dS/m which will be used as new sources of tolerance for salinity stress. These can also be used as donor parents in breeding programs for salinity tolerance. The development of mapping population can help in the identification of new gene(s)/QTL(s) responsible for salinity tolerance.

Salt-tolerant rice varieties offer great potential to grow rice in marginal lands, which are usually left fallow particularly during the dry season because of high salinity. The area under this type of land is quite substantial—approximately 0.83 million hectares in Bangladesh and over 6.7 million ha in India. In West Africa, an estimated 1.5 million hectares of cultivable mangrove swamps are affected by salinity (Jones 1986).

Evaluation of multi-QTL marker-assisted introgression process

The protocol for the simultaneous introgression of multiple QTLs was developed and verified in several backgrounds, focusing on NSIC Rc222 and also in Makassane-Sub1, IRRI 171, IRRI 110, IRRI 139, and MS11. Key innovations include the use of the crossing methodology, allowing the production of over 2000 BC-F1 seeds from a single selected F1 plant. This enables the introgression of a large number of QTLs simultaneously, in no extra time, rather than just one or two QTLs. These methodologies have been adopted and were used in the QTL deployment group to speed up the delivery of other genes such as in priority disease resistance and grain quality loci. This milestone has significant synergy with the QTL fingerprinting tool, which gives insight into additional loci that can be targeted in the MAS populations.

Incorporation of diagnostic marker information into a QTL fingerprinting database tool

The project developed a diagnostic tool where causative alleles for 27 QTLs were identified and incorporated into a fingerprinting tool. Fingerprinting capacity expanded to 50 QTLs and counting, including many abiotic stress, biotic stress, grain quality, and agronomic QTLs. This tool provides breeders a comprehensive view of the major genes found in their elite material, which in turn enables better crossing decisions and more effective breeding.

Identification of candidate genes for at least two QTLs other than SalTol based on whole-genome sequencing

Genome sequences were obtained for six donors and five recipient lines used in the mapping of salinity tolerance QTLs and accurate marker systems for a range of QTLs were developed. However, results from the QTL validation studies showed many previously reported QTLs had dubious validity. Studies to verify these QTLs yielded at least one locus that was consistent across backgrounds and salinity stress levels; efforts were undertaken to deploy this into NSIC Rc222 as an elite recipient variety and this was taken to BC5 level. Candidate genes for this QTL were identified and several were cloned, including into binary vectors, but funding and time were insufficient to conduct transgenic validation. Fine-mapping is underway as an alternative strategy for identifying candidate genes for this locus.