Salt stress reduces land and water productivity and contributes to poverty and food insecurity. Increased salinization caused by human practices and climate change is progressively reducing agriculture productivity despite escalating calls for more food. Plant responses to salt stress are well understood, involving numerous critical processes that are each controlled by multiple genes. Knowledge of the critical mechanisms controlling salt uptake and exclusion from functioning tissues, signaling of salt stress, and the arsenal of protective metabolites is advancing. However, little progress has been made in developing salt-tolerant varieties of crop species using standard (but slow) breeding approaches. The genetic diversity available within cultivated crops and their wild relatives provides rich sources for trait and gene discovery that has yet to be sufficiently utilized. Transforming this knowledge into modern approaches using genomics and molecular tools for precision breeding will accelerate the devel...

Genomics, Physiology, and Molecular Breeding Approaches for Improving Salt Tolerance.

https://www.cell.com/trends/plant-science/pdf/S1360-1385(15)00260-5.pdf

Landrace Germplasm for Improving Yield and Abiotic Stress Adaptation

Salinity is one of the most important abiotic stress affecting the world rice production. The cultivation of salinity-tolerant cultivars is the most cost-effective and environmentally friendly approach for salinity control. In recent years, CRISPR/Cas9 systems have been widely used for target-site genome editing; however, their application for the improvement of elite rice cultivars has rarely been reported. Here, we report the improvement of the rice salinity tolerance by engineering a Cas9-OsRR22-gRNA expressing vector, targeting the OsRR22 gene in rice. Nine mutant plants were identified from 14 T0 transgenic plants. Sequencing showed that these plants had six mutation types at the target site, all of which were successfully transmitted to the next generations. Mutant plants without transferred DNA (T-DNA) were obtained via segregation in the T1 generations. Two T2 homozygous mutant lines were further examined for their salinity tolerance and agronomic traits. The results showed that, at the seedling stage, the salinity tolerance of T2 homozygous mutant lines was significantly enhanced compared to wild-type plants. Furthermore, no significantly different agronomic traits were found between T2 homozygous mutant lines and wild-type plants. Our results indicate CRISPR/Cas9 as a useful approach to enhance the salinity tolerance of rice.

/pdf/enhanced-rice-salinity-tolerance-via-crispr-cas9-targeted-1ni4njb2mz.pdf

Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene

Plant diversity sustains all animal life, and the genetic diversity within plants underpins global food security. This text provides a practical and theoretical introduction to the strategies and actions to adopt for conserving plant genetic variation, as well as explaining how humans can exploit this diversity for sustainable development. Notably readable, it initially offers current knowledge on the characterization and evaluation of plant genetic resources. The authors then discuss strategies from in situ and ex situ conservation to crop breeding, exploring how these can be used to improve food security in the face of increasing agrobiodiversity loss, human population growth and climate change. Each chapter draws on examples from the literature or the authors' research and includes further reading references. Containing other useful features such as a glossary, it is invaluable for professionals and undergraduate and graduate students in plant sciences, ecology, conservation, genetics and natural resource management.

Plant Genetic Conservation

High-throughput phenotyping produces multiple measurements over time, which require new methods of analyses that are flexible in their quantification of plant growth and transpiration, yet are computationally economic. Here we develop such analyses and apply this to a rice population genotyped with a 700k SNP high-density array. Two rice diversity panels, indica and aus, containing a total of 553 genotypes, are phenotyped in waterlogged conditions. Using cubic smoothing splines to estimate plant growth and transpiration, we identify four time intervals that characterize the early responses of rice to salinity. Relative growth rate, transpiration rate and transpiration use efficiency (TUE) are analysed using a new association model that takes into account the interaction between treatment (control and salt) and genetic marker. This model allows the identification of previously undetected loci affecting TUE on chromosome 11, providing insights into the early responses of rice to salinity, in particular into the effects of salinity on plant growth and transpiration.

/pdf/salinity-tolerance-loci-revealed-in-rice-using-high-4p0a04cpqh.pdf

Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping

Improving salt tolerance of lowland rice cultivar ‘Rassi’ through marker-aided backcross breeding in West Africa

Salinity is a major constraint affecting rice productivity in rainfed and irrigated agro-ecosystems.
 Understanding salinity effects on rice production at the reproductive stage could improve adaptation for this trait. Identifying quantitative trait loci (QTLs) controlling adaptation to salinity may also accelerate breeding rice germplasm for environments prone to this stress. We used the salt tolerant landrace ‘Hasawi’ as a donor parent to generate three F2 offspring (consisting each of 500 individuals) with three African cultivars (‘NERICA-L-19’, ‘Sahel 108’ and ‘BG90-2’) used as recipient parents (RP). The F2s and F2:3s were evaluated for grain yield and other traits in saline fields. Salinity caused reduction in all measured traits across the F2-derived offspring, e.g. grain yield reduced between 65 and 73 %, but some offspring had twice the RP’s grain yield. QTL analysis revealed 75 QTLs for different traits in all 3 genetic backgrounds (GBs): 24 of them were common among all the 3 GBs while 31 were noted in 2 GBs, and 17 in one GB. ‘Hasawi’ contributed on average 49 % alleles to these QTLs. Two yield and yield related QTLs (qGY11 and qTN11) common in all 3 GBs were mapped on the same chromosomal segment suggesting these QTLs might be stable across different GBs. Four other QTLs were strongly associated with salinity tolerance with peak marker RM419, representing a potential candidate for MAS due to high LOD score and relatively large effect QTLs.

New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi, a Saudi landrace into three African cultivars at the reproductive stage

Salinity is one of the most serious factors limiting the productivity of rice crops, with adverse effects on germination, plant vigor and crop yield. A population of 300 F 5:6 recombinant inbred lines (RILs), which was derived from a cross between IR29 (indica sensitive to salinity) and Hasawi (Saudi cultivar showing salt tolerance), was evaluated at a young seedling stage under hydroponic conditions at an EC of 12 dsm -1 . Such RIL population when fixed can be repeatedly used for investigating QTLs of various phenotypes under different environments. Transgressive segregation was noted for all traits in the RILs; In all 31 RILs (10% of the 300 RILs) had tolerance level similar or better than Hasawi as determined by their standard evaluation system (SES) score of 4 or less, performance under both saline and non-saline conditions for plant height, root length, shoot dry weight and shoot fresh weight; suggesting these RILs can be rated as tolerant to salinity and are been advanced in our breeding program Quantitative trait loci (QTL) related to salt tolerance were detected using 142 F 5 RILs and single nucleotide polymorphisms (SNPs) chip composed of 384 SNP markers for indica x indica background. There were seven significant QTL related to 4 different traits associated to salt tolerance at young seedling stage. They were mapped on chromosomes 1, 2 and 6. The QTL qDW1.1, qDW2.1, qDW2.2 and qDW6.1 co-segregated with shoot dry weight and accounted between 10.6 and 42.3% of its phenotypic variation, while qPH1.1 and qPH1.2 were associated with plant height (explaining between 12.7 and 13.8% of its phenotypic variation), and qF2.1 co-segregated with shoot fresh weight (10.6% of trait variation) was accounted by SNP marker (id2007526). These QTLs had positive additive effects confirming that Hasawi alleles contributed to enhance traits related to salt tolerance at young seedling stage. The SNP markers associated with the QTLs identified in this study could be useful for further marker-aided breeding aiming at developing new rice cultivars for saline-prone agro-ecosystems

http://genbreedpublisher.com/index.php/mpb/article/download/1409/1166

Nana Kofi Abaka Amoah

Papers

Improving salt tolerance of lowland rice cultivar ‘Rassi’ through marker-aided backcross breeding in West Africa

New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi, a Saudi landrace into three African cultivars at the reproductive stage

Mapping QTLs Related to Salt Tolerance in Rice at the Young Seedling Stage using 384-plex Single Nucleotide Polymorphism SNP, Marker Sets

Mapping chromosomal regions associated with anther indehiscence with exerted stigmas in CRI-48 and Jasmine 85 cross of rice (Oryza sativa L).