Mapping of quantitative trait locus related to submergence tolerance in rice with aid of chromosome walking

Fine mapping and gene cloning in the post-NGS era: advances and prospects

Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.

Sub1 Rice: Engineering Rice for Climate Change

By the year 2100, the number of people on Earth is expected to increase by ∼50%, placing increasing demands on food production in a time when a changing climate is predicted to compromise crop yields. Feeding this future world requires scientifically informed innovations in agriculture. Here, we describe how a rice gene conferring tolerance to prolonged submergence has helped farmers in South and Southeast Asia mitigate rice crop failure during floods. We discuss how planting of this new variety benefited socially disadvantaged groups. This example indicates that investment in agricultural improvement can protect farmers from risks associated with a changing climate.

Responses of rice (Oryza sativa L.) genotypes to different levels of submergence

The study aims at identifying some submergence-tolerant rice genotypes through morphological and molecular characterization and their genetic variability analysis. Ten rice genotypes including two submergence-tolerant checks, two susceptible varieties and six advanced lines were evaluated for submergence tolerance in the laboratory and in the field during January-December 2015. The experiment was conducted in the field following randomized complete block design in a two-factor arrangement using five replications. Ten characters, viz. days to flowering, plant height, tiller number plant^-1, effective tiller plant^-1, and yield plant^-1 etc. were studied for four treatments. A significant genotype×environment interaction was observed for all traits studied in this experiment. The yield was reduced for all genotypes at a different level of submergence stress compared to control. Binadhan-11, Binadhan-12, RC 249 and RC 251 showed tolerance, whereas RC 192, RC 193 and RC 225 showed moderate tolerance in submerged condition. The phenotypic coefficient of variance (PCV) was higher than the genotypic coefficient of variance (GCV) in all the studies traits. High heritability (75-97%) was found for all traits. High heritability along with high genetic advance was found for days to flowering (45.55) and plant height (40.05). Molecular characterization of the used genotypes was done with three SSR markers viz. RM 24, and submergence specific SC3 and SUB1. SC3 was found reliable for detection of submergence tolerant genotypes due to the highest gene diversity (0.840) compared to others. The banding pattern of the submergence specific markers SC3 and SUB1 identified in Binadhan-11, Binadhan-12, RC 192, RC 193, RC 225, RC 227, RC 249, and RC 251, which possess the SUB1 gene. Finally, clustering also separates the tolerant genotypes from the susceptible by dividing them into different clusters. The identified genotypes might be useful for the breeding programme for the development of submergence tolerant as well as resistant rice variety in Bangladesh.

Comparative Transcriptional Profiling of Primed and Non-primed Rice Seedlings under Submergence Stress

Submergence stress is a limiting factor for direct-seeded rice systems in rainfed lowlands and flood-prone areas of South and Southeast Asia. The present study demonstrated that submergence stress severely hampered the germination and seedling growth of rice, however, seed priming alleviated the detrimental effects of submergence stress. To elucidate the molecular basis of seed priming-induced submergence tolerance, transcriptome analyses were performed using 4-day-old primed (selenium-Se and salicylic acid-SA priming) and non-primed rice seedlings under submergence stress. Genomewide transcriptomic profiling identified 2371 and 2405 transcripts with Se- and SA-priming, respectively, that were differentially expressed in rice compared with non-priming treatment under submergence. Pathway and gene ontology term enrichment analyses revealed that genes involved in regulation of secondary metabolism, development, cell, transport, protein, and metal handling were over-represented after Se- or SA-priming. These coordinated factors might have enhanced the submergence tolerance and maintained the better germination and vigorous seedling growth of primed rice seedlings. It was also found that many genes involved in cellular and metabolic processes such as carbohydrate metabolism, cellular, and metabolic biosynthesis, nitrogen compound metabolic process, transcription, and response to oxidative stress were induced and overlapped in seed priming treatments, a finding which reveals the common mechanism of seed priming-induced submergence tolerance. Taken together, these results may provide new avenues for understanding and advancing priming-induced responses to submergence tolerance in crop plants.

Comparative Transcriptional Profiling of Primed and Non-primed Rice Seedlings under Submergence Stress

Submergence stress is a limiting factor for direct-seeded rice systems in rainfed lowlands and flood-prone areas of South and Southeast Asia. The present study demonstrated that submergence stress severely hampered the germination and seedling growth of rice, however, seed priming alleviated the detrimental effects of submergence stress. To elucidate the molecular basis of seed priming-induced submergence tolerance, transcriptome analyses were performed using 4-day-old primed (selenium-Se and salicylic acid-SA priming) and non-primed rice seedlings under submergence stress. Genomewide transcriptomic profiling identified 2371 and 2405 transcripts with Se- and SA-priming, respectively, that were differentially expressed in rice compared with non-priming treatment under submergence. Pathway and gene ontology term enrichment analyses revealed that genes involved in regulation of secondary metabolism, development, cell, transport, protein, and metal handling were over-represented after Se- or SA-priming. These coordinated factors might have enhanced the submergence tolerance and maintained the better germination and vigorous seedling growth of primed rice seedlings. It was also found that many genes involved in cellular and metabolic processes such as carbohydrate metabolism, cellular, and metabolic biosynthesis, nitrogen compound metabolic process, transcription, and response to oxidative stress were induced and overlapped in seed priming treatments, a finding which reveals the common mechanism of seed priming-induced submergence tolerance. Taken together, these results may provide new avenues for understanding and advancing priming-induced responses to submergence tolerance in crop plants.

Construction of a comparative RFLP map of Echinochloa crus-galli toward QTL analysis of flooding tolerance

To analyze quantitative trait loci (QTLs) affecting flooding tolerance and other physiological and morphological traits in Echinochloa crus-galli, a restriction fragment length polymorphism (RFLP) map was constructed using 55 plants of the F(2) population ( E. crus-galli var. praticola x E. crus-galli var. formosensis). One hundred forty-one loci formed 41 linkage groups. The total map size was 1,468 cM and the average size of linkage groups was 35.8 cM. The average distance between markers was 14.7 cM and the range was 0-37.2 cM. Early comparisons to the genetic maps of other taxa suggest appreciable synteny with buffelgrass ( Pennisetum spp.) and sorghum ( Sorghum spp.). One hundred ninty-one F(2) plants were used to analyze QTLs of flooding tolerance, plant morphology, heading date, number of leaves, and plant height. For flooding tolerance, two QTLs were detected and one was mapped on linkage group 24. Other traits, including plant morphology, heading date, number of leaves, and plant height were highly correlated. Three genomic regions accounted for most of the mapped QTLs, each explaining 2-4 of the significant marker-trait associations. The high observed correlation between the traits appears to result from QTLs with a large contribution to the phenotypic variance at the same or nearby locations.