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.

Exploring the Genetic Diversity among Weedy Rice Accessions Differing in Herbicide Tolerance and Allelopathic Potential

Increasing agricultural productivity is indispensable to meet future food demand. Crop improvement programs rely heavily on genetic diversity. The success of weeds in the ecosystem can be attributed to genetic diversity and plasticity. Weedy rice, a major weed of rice, has diverse morphology and phenology, implying wide genetic diversity. Study was conducted to genotype weedy rice accessions (n = 54) previously phenotyped for herbicide tolerance and allelopathic potential using 30 SSR markers. Cultivated rice (CL163, REX) and allelopathic rice (RONDO, PI312777, PI338047) were also included in the study. Nei’s genetic diversity among weedy rice (0.45) was found to be higher than cultivated rice (0.24) but less than allelopathic rice (0.56). The genetic relationship and population structure based on herbicide tolerance and allelopathic potential were evaluated. Herbicide-tolerant and susceptible accessions formed distinct clusters in the dendrogram, indicating their genetic variation, whereas no distinction was observed between allelopathic and non-allelopathic weedy rice accessions. Weedy rice accession B2, which was previously reported to have high allelopathy and herbicide tolerance, was genetically distinct from other weedy rice. Results from the study will help leverage weedy rice for rice improvement programs as both rice and weedy rice are closely related, thus having a low breeding barrier.

Identification of bacterial blight resistance genes in rice landraces from Yunnan Province, China

Bacterial blight (BB), a serious bacterial disease caused by pathogen Xanthomonas oryzae pv. oryzae (Xoo) affects rice growth and yield. Yunnan Province is regarded as a center of rice diversity in China and indeed the world, and has abundant rice landrace resources, which may offer prospective candidate donors in rice improvement and breeding. In this study, a set of 200 rice landraces were evaluated to determine their resistance to 10 pathogenic Xoo strains resistance by the leaf-clipping method. The results indicated that the tested rice landraces had different resistance levels against different Xoo strains. Multiple comparisons showed that the Xoo strain PXO99 was virulent to the tested rice landraces. Sixty-six rice landraces conferred resistance against at least one Xoo strain. These resistant rice landraces screened were then performed the presence of 14 cloned BB resistance genes by closely linked molecular markers and designed specific primers. The results showed that none of these resistant accessions contained xa13, Xa21, Xa27, and Xa45(t) homologous fragments, while 9, 24, 4, 7, 9, 15, 1, 5, 4 and 27 accessions contained Xa1, Xa2/Xa31(t), Xa14, Xa3/Xa26, Xa4, xa5, Xa7, Xa10, Xa23 and xa25 homologous fragments, respectively. Sequence analysis further revealed that nucleotide variations around functional nucleotide polymorphisms region were observed within these accessions containing the Xa1, Xa2/Xa31(t), Xa14, Xa3/Xa26, Xa4, xa5, Xa10, Xa23 and xa25 homologous fragments. These results along with phenotypic resistance spectrum supported that these accessions carried nine resistance homologous genes. Only one accession (Qishanggu_Wenshan) carried the Xa7 resistance gene. We also found that some resistant rice landraces, especially Xilandigu_Baoshan, and Laoyaling_Lincang without the above resistance genes, which mediated broad spectrum resistance to multiple Xoo strains, were identified as potential sources for breeding rice lines resistance to BB.

Rice crop response to site variability in a multi-locational trial: A call for site specific management

Yield is a net expression of genotype (G) x environment (E) interactions including management. However, the segregation of 'E' into respective causes is seldom done while 'G' is a constant. Soil is a component of 'E' with imminent variability in attributes among multiple locations. Data on yield response of varieties to a set of treatments in different soils from multi-locational yield maximisation trial under All India Coordinated Rice Improvement Project were regularly gathered. A dataset pertaining to a trial conducted in Karaikal district of Puducherry Union Territory was analysed to ascertain the site-specific crop responses with inherent variability in soils. Rice varieties, ADT 46, BPT 5204 and CR 1009 were tested for responses at 17 sites with farmer fertiliser practices (FFP), regional recommended fertiliser dose (RDF) and software, 'Nutrient Expert®' (2016) (NE) derived fertiliser quantities. Analysis of variance showed that test sites explained 59.3% variability in yield. A multivariate technique, Factor Analysis extracted two factors, which are linear combinations of soil attributes those explained 76% of variance in soils. Factor scores classified soils into four groups, owing to variability in soil properties. Soil texture influenced yield significantly (across varieties and treatments) (R2 = 11.1%). Sites varied in excess duration in nursery ranging from 2 - 26 days. However, this excess duration reduced number of panicles m-2 only in CR 1009 (r = -0.328**). General linear model with sites and treatments as fixed factors, their interactions and panicles m-2 as covariate predicted better (R2 = 90.3%) with their significant contribution to the model. The order of R2 (%) was Sites (59.3) > Varieties (27.4) > Treatments (13.6%) in explaining variability in yield highlighting site-specific responses. Mean differences between ADT 46 and BPT 5204; BPT 5204 and CR 1009 were significant. Yield significantly changed across sites and treatments when fertiliser management shifted from non-specific (FFP) to site-specific NE based calculations through RDF (region specific). Results of this trial placed emphasis on soil test-based crop management to realise the uniform best, which clearly is site specific crop management.

Exploring the Genetic Diversity Among Weedy Rice Accessions Differing in Herbicide Tolerance and Allelopathic Potential

Increasing agricultural productivity is indispensable to meet future food demand. Crop im-provement programs rely heavily on genetic diversity. The success of weeds in the ecosystem can be attributed to genetic diversity and plasticity. Weedy rice, a major weed of rice, has diverse morphology and phenology, implying wide genetic diversity. Study was conducted to genotype weedy rice accessions (n =54) previously phenotyped for herbicide tolerance and allelopathic potential using 30 SSR markers. Cultivated rice (CL163, REX) and allelopathic rice (RONDO, PI312777, PI338047) were also included in the study. Nei’s genetic diversity among weedy rice (0.45) was found to be higher than cultivated rice (0.24) but less than allelopathic rice (0.56). The genetic relationship and population structure based on herbicide tolerance and allelopathic po-tential were evaluated. Herbicide-tolerant and susceptible accessions formed distinct clusters in the dendrogram, indicating their genetic variation, whereas no distinction was observed between allelopathic and non-allelopathic weedy rice accessions. Weedy rice accession B2, which was previously reported to have high allelopathy and herbicide tolerance, was genetically distinct from other weedy rice. Results from the study will help leverage weedy rice for rice improvement programs as both rice and weedy rice are closely related, thus having a low breeding barrier.

Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement

Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8–10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.

Phenotypic Characterization of Diverse Rice Fertility Restorers

Characterization of restorer lines of rice based on seedling and plant morphology contributes in assessment of varietal identity and further its utilization in development of hybrids. With this objective the work was carried over with 90 restorer lines with three replications during Kharif season 2018. The experiment conducted under Rice Improvement Project at Seed Breeding Farm, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur (M.P.).Out of 41 morphological traits as per DUS guidelines, variability was reported for all traits except leaf sheath anthocyanin colouration, presence of leaf auricle, presence of leaf collar, presence of leaf ligules, white colour of leaf ligules, absence of stem anthocyanin colouration of internodes, male sterility and presence of secondary branching in panicle. The genotypes Mahamaya, ANP-526 and ANP-553 revealed distinctness for most of the traits.

Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives

Food crop production and quality are two major attributes that ensure food security. Rice is one of the major sources of food that feeds half of the world’s population. Therefore, to feed about 10 billion people by 2050, there is a need to develop high-yielding grain quality of rice varieties, with greater pace. Although conventional and mutation breeding techniques have played a significant role in the development of desired varieties in the past, due to certain limitations, these techniques cannot fulfill the high demands for food in the present era. However, rice production and grain quality can be improved by employing new breeding techniques, such as genome editing tools (GETs), with high efficiency. These tools, including clustered, regularly interspaced short palindromic repeats (CRISPR) systems, have revolutionized rice breeding. The protocol of CRISPR/Cas9 systems technology, and its variants, are the most reliable and efficient, and have been established in rice crops. New GETs, such as CRISPR/Cas12, and base editors, have also been applied to rice to improve it. Recombinases and prime editing tools have the potential to make edits more precisely and efficiently. Briefly, in this review, we discuss advancements made in CRISPR systems, base and prime editors, and their applications, to improve rice grain yield, abiotic stress tolerance, grain quality, disease and herbicide resistance, in addition to the regulatory aspects and risks associated with genetically modified rice plants. We also focus on the limitations and future prospects of GETs to improve rice grain quality.

ANALISIS SESAR-SESAR MAJOR SEMENANJUNG MALAYSIA DENGAN TEKNIK GRAVITI DEKONVOLUSI EULER 3D

The application of biotechnology in upland rice improvement programs depends on the availability of efficient regeneration protocols. Although protocols for shoot regeneration of upland rice are available, none has been reported for pigmented cultivars. This study reports on a protocol for callus induction and regeneration of Tadong, a pigmented upland rice cultivar from Sabah. For callus induction, immature embryos were cultured on media containing 2,4-Dichlorophenoxyacetic (2,4-D) at various concentrations (0 – 2.5 mg/L) and on different types of media (MS; MSB5; N6B5; N6). To induce shoot regeneration, callus explants were cultured on MS medium supplemented with combinations of 6-Benzylaminopurine (BAP) at various concentrations (0 – 3.0 mg/L) and 1-Naphthaleneacetic acid (NAA) at 1.0 mg/L. To induce shoot development, callus explants were pre-treated with Thidiazuron (TDZ) at various concentrations (0-1.0 mg/l) and exposed to different desiccation periods (0 – 72 hours). 2,4-Dichlorophenoxyacetic at 2.5 mg/L and N6B5 medium resulted in the highest percentages of explant forming callus which were 60.3 ± 17.0 % and 58.7 ± 9.8 % respectively. The regeneration media failed to induce shoot on callus explants, instead, green spots were formed on the surface of the callus. The green spots were stimulated to develop into shoots when the callus explants were pre-treated with 0.5 mg/L TDZ or exposed to partial desiccation for 24 h, the percentages of explant forming shoot were 35.7 ± 4.8 % and 47.7 ± 6.8 % respectively. Shoots developed into complete plants on hormone-free MS medium and acclimatized.