Tropical Japonica Rice Varieties Research Articles

Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing.

Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study, the length of insertions/deletions variation greater larger than 10 bp from 10 Oryza sativa ssp. indica rice and 10 Oryza sativa ssp. tropical japonica rice were extracted by using the Nipponbare genome as a reference. A total of 118 primer pairs which were almost evenly distributed on each chromosome corresponding to the loci of InDels were designed by the Primer 5 program. We confirmed 85 InDel markers from 60 rice varieties, including indica and tropical japonica, by running polyacrylamide gels. The InDel markers function like SSRs in identifying hybrids, calculating genetic distance, constructing the genetic linkage map, and gene mining. The InDel markers developed in this study might help in genetic studies and to investigate the tropical japonica rice varieties.

Optimizing Agrobacterium-Mediated Transformation and CRISPR-Cas9 Gene Editing in the tropical japonica Rice Variety Presidio.

Bottlenecks in plant transformation and regeneration have slowed progress in applying CRISPR/Cas-based genome editing for crop improvement. Rice (Oryza sativa L.) has highly efficient temperate japonica transformation protocols, along with reasonably efficient indica protocols using immature embryos. However, rapid and efficient protocols are not available for transformation and regeneration in tropical japonica varieties, even though they represent the majority of rice production in the U.S. and South America. The current study has optimized a protocol using callus induction from mature seeds with both Agrobacterium-mediated and biolistic transformation of the high-yielding U.S. tropical japonica cultivar Presidio. Gene editing efficiency was tested by evaluating knockout mutations in the phytoene desaturase (PDS) and young seedling albino (YSA) genes, which provide a visible phenotype at the seedling stage for successful knockouts. Using the optimized protocol, transformation of 648 explants with particle bombardment and 532 explants with Agrobacterium led to a 33% regeneration efficiency. The YSA targets had ambiguous phenotypes, but 60% of regenerated plants for PDS showed an albino phenotype. Sanger sequencing of edited progeny showed a number of insertions, deletions, and substitutions at the gRNA target sites. These results pave the way for more efficient gene editing of tropical japonica rice varieties.

An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies.

Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding.

Response of U.S. Rice Cultivars Grown under Non-Flooded Irrigation Management

Achieving food security along with environmental sustainability requires high yields with reduced demands on irrigation resources for rice production systems. The goal of the present investigation was to identify traits and germplasms for rice breeding programs that target effective grain production (EGP) under non-flooded field systems where the crop can be subjected to intermittent water stress throughout the growing season. A panel of 15 cultivars was evaluated over three years regarding phenological and agronomic traits under four soil moisture levels ranging from field capacity (29% volumetric water content; VWC) to just above the wilting point (16% VWC) using subsurface drip irrigation. An average of 690 ha-mm ha−1 water was applied for the 30% VWC treatment compared to 360 ha-mm ha−1 for the 14% VWC treatment. The average soil moisture content influenced several traits, including grain quality. Regression analysis identified six traits that explained 35% of the phenotypic variability of EGP. Four varieties (PI 312777, Francis, Zhe 733, and Mars) were found possessing significant slopes for 10 or more traits that respond to a range in soil moisture levels, indicating that they may offer promise for future rice breeding programs. Furthermore, based on the contrasting responses of four parent cultivars, two mapping populations were identified as potential genetic resources for identifying new quantitative trait loci/genes for improving EGP of tropical japonica rice varieties.

Development and Characterization of a Large Mutant Population of a Rice Variety Katy for Functional Genomics Studies and Breeding

The availability of a large mutant population is an important genetic resource for functional genomic studies and breeding. Katy, a publicly available long grain tropical japonica rice variety with an excellent package of disease resistance and suitable agronomic traits, was used to develop a large mutant population. A combination of ethyl methane sulfonate (EMS), fast neutron (FN), and gamma irradiation (60Co) treatments were applied at varying dosages to develop the population. Approximately 7500 rice seeds were each treated with EMS (0.4%, 0.8%, and 1.2%) and 60Co (200 Gy), and approximately 10,000 rice seeds were exposed to 7.7 Gy, 26.3 Gy, and 49.4 Gy dosages of FN. Mutation effects were initially evaluated at the M2 generation by assessing chlorophyll biosynthesis deficiencies. The mutation effects of each line were detected at 1.04% for 0.4% EMS, 5.04% for 0.8% and 1.2% EMS, 2.9% for 26.3 Gy FN, 3.2% for 49.4 Gy FN, and 5.04% for 60Co 200 Gy for the M2 population. After seeds were advanced to M4 using a single seed breeding strategy, the genotype identity of 189 randomly selected lines was verified with nine simple sequence repeat markers and 96 randomly selected lines were evaluated for mutant morphological phenotypes. The analysis uncovered slightly higher frequencies of morphological mutants at M4 than was observed in the M2 generation. These findings suggest that the Katy putative mutant population consisting of 23,558 individuals is a potential asset for rice functional genomics studies and breeding.

Genetic variability of nitrogen use efficiency in rainfed upland rice

In sub-Saharan Africa and in Madagascar, upland rice is mostly grown for subsistence by resource-poor farmers in low-input production systems with low yields. In this context, soil nitrogen availability is a major limiting factor. To determine the appropriate breeding strategy to improve nitrogen use efficiency (NUE), the genetic variability and the level of G×N interaction of NUE need to be evaluated. NUE and its components are complex quantitative traits and the study of their relationship with other simpler traits should help understand the mechanisms involved in NUE and identify ways to improve it. A study was conducted at mid-altitude in Madagascar using 13 adapted tropical japonica rice varieties over three cropping seasons with two contrasted levels of applied N (high N with 90–120kgNha−1 as urea and low N without mineral fertilizer) in rainfed upland conditions. Year×N and Year×G interactions were significant due to contrasted rainfall distributions across the three cropping seasons. Agronomic efficiencies of N fertilization were low (11.5kg grain kg−1N in the best year) because of N loss through leaching or volatilization. Our results also suggest gaseous loss of N by plants between flowering and harvest, particularly under the high N treatment. The experiment revealed significant genetic variability for NUE, nitrogen uptake efficiency (NUPE) and nitrogen utilization efficiency (NUTE) in both high N and low N treatments but a low level of G×N interaction. The variation in NUPE accounted for more of the variation in NUE than the variation in NUTE. There was no correlation between NUPE and NUTE, either under high N or under low N. We found no negative relationship between grain yield and grain N concentration under low N. The relationship between NUE and agronomic and N-related traits differed from one year to the next, illustrating the plasticity of the contribution of the different agronomic traits to NUE as a function of the contrasted climatic conditions (particularly the rainfall distribution pattern). However, two traits, the number of panicles per m2 and the harvest index were consistently positively correlated with NUE. The difference between total N uptake at flowering and at harvest was positively correlated with NUE, particularly under the low N treatment.

Identification of Quantitative Trait Loci (QTL) for Awn, Incomplete Panicle Exertion and Total Spikelet Number in an F2 Population Derived from A Backcross Inbred Line, Bio-148, and the Recurrent Parent, IR64

An F2 rice population developed from a cross between a backcross inbred line (BIO-148) and its recurrent parent (IR64) was used to identify quantitative trait loci (QTL) for awn, panicle exertion and total spikelet number. BIO-148 is a BC2F8 line derived from a cross between IR64 (a high-yielding lowland rice variety) and Gajah Mungkur (an upland tropical japonica rice variety). Two hundred plants were grown in the greenhouse, and their DNAs were isolated for genotyping using SSR markers. Panicle exertion was observed during the grain-filling stage. The awn length of the seed and the total spikelet number per panicle were observed after harvesting. A total of four QTLs were identified using single-marker regression with LOD>3, explaining 8.4-18.1% of phenotypic variation. A QTL for awn was identified on Chromosome 8 . A QTL for incomplete panicle exertion was identified on Chromosome 4. Two QTLs for total spikelet number were identified on Chromosome 4, in which the BIO-148 allele contributed to a higher number of spikelets per panicle. The QTLs identified in this study will be useful in the improvement of yield potential for modern lowland indica rice varieties by harnessing the hidden useful alleles from upland tropical japonica rice varieties.

English

Nitrogen use efficiency (NUE) is an important characteristic for increasing the yield and quality of rice grains and reducing the use of nitrogen fertilizers. This study evaluated parameters that contribute to NUE in two tropical japonica rice varieties contrasting in nitrogen remobilization efficiency (NRE) and nitrate-uptake kinetics: IAC-47 (bred for high-input farming), and Piaui (a landrace from the state of Maranhao, Brazil). The two varieties were grown with and without N supplementation at anthesis stage. Both varieties received urea equivalent to 60 kg N ha -1 in the first ten days after planting (DAP) and a subset of the two varieties received a supplementation with 40 kg N ha -1 at anthesis stage, composing a treatment with supplementation (Ts). The control treatment (Tc) was constituted of the plants that did not receive nitrogen supplementation at anthesis. We analyzed the nitrogen soluble fractions, soluble sugars, dry matter production, total N, crude protein in grains, NUE parameters, and expression and activity of glutamine synthetase (GS). The N uptake after anthesis affected the total N content in the shoots and grains of both rice varieties. In treatments with and without N supplementation, the nitrogen uptake efficiency (NUpE) was higher in IAC-47 than in Piaui plants. The NRE, a desirable characteristic for plants grown with low N input, was around two times higher in the Piaui plants that were not supplemented with N during anthesis. panicles of piaui plants grouwn without N supplementation presented higher expression of the glutamine synthetase gene OsGS1.3 post-anthesis. The results indicate that NRE is the primary factor contributing to NUE in rice varieties adapted to a low N supply, whereas improved varieties exhibit a higher NUpE.

Selection Criteria, Yield Relationship with Component Traits and Grouping of Tropical Japonica, Indica Lines and Derived Hybrids of Rice (Oryza sativa L.)

Forty-five rice lines comprising of thirty derived hybrid lines obtained from ten tropical Japonica, three Indica and two national checks viz. Pusa Basmati 1121 and Sarjoo-52 were evaluated for selection parameters, yield contributing components and genetic divergence. Fifteen quantitative and three qualitative traits were studied from experimentation with randomized block design during Kharif 2011. The phenotypic coefficient of variability was higher than genotypic coefficient of variability for all of the traits. The highest estimates of broad sense heritability coupled with genetic advance in per cent of mean was recorded for spikelets per panicle, plant height followed by L:B ratio, spikelets per panicle, grains per panicle, biological yield per plant, flag leaf area, days to 50% flowering, plant height which might be due to the additive nature of gene action. Such results indicated that these traits will be reliable for the effective selection. Highly positive and significant correlation was observed at both phenotypic and genotypic level between grain yield per plant and biological yield per plant, followed by panicle bearing tillers per plant, spikelet fertility, panicle length, 1000- grain weight, grains per panicle, panicle weight, flag leaf length, spikelet per panicle, flag leaf area, kernel length, flag leaf width, days to 50% flowering, and harvest index. This relationship reflected that grain yield and aforesaid economic traits can be increased simultaneously in breeding programme to develop high yielding Indica as well as Tropical Japonica rice varieties. Whole genotypes grouped in 8 non-overlapping clusters exhibited maximum genetic diversity between clusters III i.e., TJ- 64897 × NDR-359, TJ-64897 × CSR36, TJ-64897 × PB-1 and VIII i.e., TJ-11010 × NDR359, TJ-11010 × PB-1, TJ-16081 × NDR-359, TJ-16081 × PB-1. These clusters also stand for early days to flowering, short slender, second highest harvest index and panicle bearing tillers per plant, spikelets per panicle, grains per panicle, spikelet fertility, 1000- grain weight, long bold slender, biological yield per plant, and grain yield per plant. These genotypes showing higher mean performance for aforesaid traits can be exploited for enhancing hybrid vigour of desired New Plant Type with higher number of panicle bearing tillers per plant, spikelet per panicle and grains per spike in Indica as well as Tropical Japonica rice varieties for achieving higher yield. DOI: http://dx.doi.org/10.3329/sja.v11i2.18399 SAARC J. Agri., 11(2): 17-32 (2013)

Detection of a novel quantitative trait locus for cold tolerance at the booting stage derived from a tropical japonica rice variety Silewah

Cold stress at the booting stage in rice induces spikelet sterility because of aberrant microspore development, which often seriously damages seed production. Some breeding lines with high cold tolerance were developed by using tropical japonica variety Silewah as a donor of cold tolerance; however, the genetic factors that confer cold tolerance of this variety have not been comprehensively analyzed. In this study, phenotypic and molecular characterization of novel cold-tolerant strains derived from crosses with Silewah was performed to identify quantitative trait loci (QTLs) responsible for cold tolerance. Molecular marker analysis revealed that 2 cold-tolerant strains carried chromosomal segments of Silewah at the same genomic regions on chromosomes 3, 4 and 11. Single marker analysis in segregating population confirmed that the allele of Silewah on chromosome 3 (qCTB3-Silewah) conferred cold tolerance. The effect of qCTB3-Silewah was supported by the fact that this allele had been a target of selection during developing a breeding line by phenotypic selection from backcrossed progenies with an elite variety as a recurrent parent. qCTB3 is a different QTL from those reported for Silewah previously, suggesting that different QTLs might be exploited in different breeding programs depending on the genetic backgrounds and environmental conditions.

Field evaluation of upland rice lines selected for QTLs controlling root traits

A marker-assisted back-cross (MABC) programme was used to introgress four root quantitative trait loci (QTLs) from the tropical japonica rice variety Azucena into the Indian upland rice variety, Kalinga III. Previously we tested the products for root traits and reported that the introgressed QTL9 (on chromosome 9) significantly increased root length in the new genetic background. Here we describe field testing for agronomic traits in near-isogenic lines (NILs) that differ for introgressed QTLs. Four NILs were selected and characterised in replicated field experiments in eastern and western India over 3 years. They were tested by upland farmers in a target population of environments (TPE) in three states of eastern India, over 2 years. NILs out-performed Kalinga III for grain and straw yield and there was interaction between the genotypes and the environment (G × E). No effect was found for the root QTL9 on grain or straw yield, however, the presence of several introgressions significantly improved both traits. Some of this effect was due to introgression of Azucena alleles at non-target regions. Overall, the Azucena introgressions increased straw yield more than grain yield. While it has yet to be demonstrated whether this effect is due to improved root systems, this finding fits with the assumption that introgressed genes are involved in partitioning of biomass to the roots and stems, rather than to the grain. The NILs could replace Kalinga III for cultivation in medium upland environments in eastern India.

Development of TGMS lines for developing two-line rice hybrids for the tropics

A breeding program was initiated at the International Rice Research Institute (IRRI) in 1990 to develop thermosensitive genic male sterile (TGMS) rice lines for developing two-line rice hybrids for the tropics. The TGMS trait was transferred from a temperate japonica TGMS mutant, Norin PL 12, to indica and tropical japonica rice varieties using the pedigree selection procedure. Six new TGMS rice lines adapted to tropical conditions were developed which showed complete pollen and spikelet sterility when maximum temperature was higher than 30 °C 1–2 week after panicle initiation. However, up to 85.5% spikelet fertility was observed when these lines were exposed to 26–29 °C during the critical stage. Using two of these TGMS lines, some heterotic rice hybrids showing 1–1.6 t/ha higher grain yield than the inbred check varieties were identified in unreplicated observational yield trial conducted at IRRI. Two of the six two-line hybrids yielded significantly higher than the check variety in a replicated preliminary yield trial.