Novel Sequencing and Genomic Technologies Revolutionized Rice Genomic Study and Breeding

Rice is one of the most important food crops worldwide. Population growth and climate change posed great challenges for further rice production. In the past decade, we have witnessed an explosive development in novel sequencing and genomic technologies. These technologies have been widely applied in rice genomic study and improvement processes, and contributed greatly to increase the efficiency and accuracy of rice breeding. On the other hand, novel sequencing and genomic technologies also promote the shift of breeding schemes from conventional field selection processes to genomic assisted breeding. These technologies have revolutionized almost every aspect of rice study and breeding. Here, we systematically sorted out and reviewed the progress and advancements of sequencing and genomic technologies. We further discussed how these technologies were incorporated into rice breeding practices and helped accelerate the rice improvement process. Finally, we reflected on how to further utilize novel sequencing and genomic technologies in rice genetic improvement, as well as the future trends of advancement for these technologies. It can be expected that, as the sequencing and genomic technologies will develop much more quickly in the future, and be combined with novel bioinformatics tools, rice breeding will move forward into the genomic assisted era.

Introgression Progress for Phenotypic Traits and Parent-progeny Diversity at Advanced Segregation Population From Oryza Barthii and Oryza Glaberrima/oryza Sativa Crosses

Rice is a cereal staple of global fame and importance. Oryza barthii, a wild species holds significant traits and its utilization in rice breeding is rare. This study traced introgression trend of heritable traits in the offspring of O. barthii with an Africa-Asian progenitor to F8 and assessed diversity between the parents and the F8 population. Significant (P<0.05) genotypic variation existed for all the traits except tiller number, panicle/meter squared, grains/panicle and 1000 grain weight. Grains/panicle and days to 50% flowering had respective least (3.34%) and highest (96.32%) broad sense heritabilities. All traits had lower GCV compared to PCV. The least (5.28% and 8.05%) and the highest (90.8% and 98.1%) GCV and PCV were respectively from grains/panicle and tiller number. Clear variations on the panicles and grains include: variations in sizes, shapes, colours, presence or absence of awns. The total variance explained by five principal component axes was 80.1%. Plant height at maturity was the only trait with significant (p ≤ 0.01) correlation and regression between F6 and F7. Progenies resemblance to Parent 1(IRGC 104084) retrogressively declined but parent-offspring to parent 2 (TGS 25) progressively increased from F6 to F8. Three visible groups of rice type in this study were: the O. barthii (11%), O. sativa (67%) and the intermediate group (22%). This research has added to rice genetic resources; an investigation of the nutritional status of the progenies would be an interesting research.

A stepwise route to domesticate rice by controlling seed shattering and panicle shape

Rice (Oryza sativa L.) is consumed by more than half of the world’s population, but despite its global importance the mechanisms of domestication remain unclear. During domestication, wild rice (O. rufipogon Griff.) was transformed by acquiring non-seed-shattering behaviour, an important genetic change that allowed humans to increase grain yield. However, we show previously identified loci, sh4 and qSH3, are individually insufficient to explain loss of seed shattering nor increases in harvest yield in wild rice. We identify the complementary interaction of key mutations for abscission layer interruption and panicle architecture that were causal in the early domestication of Asian rice. An interruption of abscission layer formation requires both sh4 and qSH3, which presents an apparent barrier to selection of shattering loss. We identified the causal single nucleotide polymorphism at qSH3 within a seed-shattering gene OsSh1 conserved in indica and japonica subspecies, but absent in the circum-aus group of rice. We demonstrate through harvest experiments that seed-shattering alone does not significantly impact yield. Instead, we observed yield increases under a SRR3-controlled closed panicle formation, which is augmented by the integration of sh4 and qSH3 alleles causing a slight inhibition of abscission layer. Complementary manipulation of seed shattering and panicle shape result in a panicle structure that is mechanically stable. We propose a stepwise route in the earliest phase of rice domestication in which selection for visible SRR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3 and leading to loss of shattering.Significance StatementRice is one of the most important crops worldwide. Loss of seed shattering in domesticated rice, previously attributed to single mutations such as in sh4, is considered the principal genetic change which resulted in yield increases. However, we show that sh4 is insufficient on its own to cause abscission layer disruption and other genes, such as qSH3 are required, making mechanisms for the initial selection of non-shattering unclear. We show that shattering loss in wild rice genetic backgrounds does not increase yields. We identify an interaction in which a second trait, closed panicle formation controlled by SPR3, both increases yield and facilitates recruitment of sh4 and qSH3 which synergistically augment yield, leading to a stepwise route for rice domestication.

Screening of rice proteins using 2-d gels after inoculation with Rhizotonia solani

Sheath blight caused by Rhizotonia solani is described as the second major disease affecting rice. Genetic resistance to R. solani the ideal control measure is hampered because of the difficulty in identifying adequate resistance sources under typical selection conditions. Proteomic analysis techniques using two-dimensional gels (2D-PAGE) allow the study or monitoring of global changes in protein expression under normal and stress conditions. In this work, we compared rice leaves protein expression patterns of two Venezuelan varieties 12, 24 and 48 h after inoculation with R. solani. Approximately 400 and 300 protein spots stained with Sypro Ruby were reproducibly resolved across gel replicates, for PALMAR and FONAIAP-2000, respectively. Forty proteins out of a total 49 were identified for PALMAR variety, with thirty-two up-regulated protein spots and 8 down-regulated. Twenty-six proteins out of a total 33 were identified for FONAIAP-2000 variety, with seven up-regulated protein spots and 19 down-regulated. RuBisCo was the protein most identified (48% and 82% of the detected proteins for PALMAR and FONAIAP-2000, respectively). Other identified proteins showing variations were ATPase beta subunit, UDP-glucose anthocyanin 5-O-glucosyltransferase, RNA-binding protein, putative transkelotase 1, putative ferredoxin-NAPD(H) oxide-reductase, and putative 33kDa oxygen evolving protein photosystem II. Based on our results, rice response to R. solani could be described where energy is required to induce a defense and it is supplied by proteins involved in energy metabolism. According to this, proteomic could provide information and insights on the response of rice to challenge with R. solani and other pathogens.