A naturally de novo-evolved gene contributes to rice grain shape difference between indica and japonica
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE218565 | GEO | 2023/08/20
REPOSITORIES: GEO
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Project description:Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population. Only 8 QTLs for grain length or grain width were detected in the F2 population, versus 47 in the CSSL population and 65 in the BC4F2 population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.
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Project description:This experiment was designed to identify transcribed regions of both japonica and indica rice chromosome 10. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 750,282 and 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogating the japonica and the indica chromosome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: other
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2017-02-09 | GSE81946 | GEO
Project description:This article used seven characters from the 2D image analysis to dissect the genetic architecture underlying rice grain shape in one japonica × indica population consisting of 215 recombinant inbred lines. Two-dimensional (2D) digital image analysis is efficient for investigating the rice grain shape characters in large genetic and breeding populations. In this study, we used 2D image analysis to investigate seven characters, i.e., grain length (GL), grain width (GW), length-to-width ratio (LW), grain area (GA), grain circumference (GC), grain diameter (GD), and grain roundness (GR), in one japonica × indica genetic population consisting of 215 recombinant inbred lines. GL and GW can be recorded manually as well, and have been extensively used together with LW (i.e., GL/GW) in genetic studies on grain shape. GC and GA can be hardly measured manually, and have not been used together with GD and GR. Results indicated that the seven characters could be precisely measured by 2D image analysis, genotype by environment interaction was low, and heritability was high. Each character was controlled by a few major stable genes and multiple minor additive genes. A total of 51 QTL were detected for the seven characters across four diverse environments, 22 from GL, GW, and LW, the three traditional characters, and 29 from the other four characters. The 51 QTL were clustered in eighteen marker intervals. Comparing with previous studies and analyzing the stability of identified QTL, we found six non-reported marker intervals, one each on chromosomes 2 and 3, and two each on chromosomes 6 and 8. The newly identified loci and the large-scale phenotyping system would greatly improve our knowledge about the genetic architecture and the future rice breeding on grain shape.
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Project description:Rice (Oryza sativa L.) is the main staple food for nearly half of the world’s population. Cereals, especially rice is deficient in micronutrients such as Fe. However, rice genotypes differ in grain Fe concentration (Panda B, et.al. Am J Plant Sci. 2014;5:2829-41. doi: 10.4236/ajps.2014.518299). The present study is focused on identification of gene(s) involved in Fe accumulation in developing rice grain through high throughput RNA-seq technology and to understand the basis of differential Fe accumulation in developing rice grain. Two cultivars of rice viz. Sharbati (high Fe) and Lalat (low Fe) differing in grain iron concentration were used in the study. Root and grain transcriptome sequences of these two cultivars (at mid-grain filling stage) were generated using RNA-Seq (Illumina Hiseq 2000 platform). For each genotype, on an average 9.7 and 7 Gb data was generated for grain and root samples, respectively. The short reads were aligned against the Nipponbare reference genome (IRGSP build 5.0), thereby successfully mapping 95% and 67% of the reads from grain and root samples, respectively. Genes known to be involved in Fe metabolism were analyzed for expression. Among the genes coding for phytosiderophore synthesizing enzymes, OsNAS1 and OsNAAT2 showed higher expression in the grains of Sharbati while OsDMAS1 had higher expression in its root. Of the 18 yellow-stripe like (YSL) genes in rice, only 11 were found to be expressed in the two cultivars. Out of these, 2 (OsYSL2 and OsYSL 8) were up-regulated in the grains of Sharbati highlighting their importance in the uptake of Fe from soil and its accumulation in the developing grain. Two other genes (OsFRO1 and OsIRT1) known to be involved in Fe uptake by the root were also found to be highly expressed in the root of Sharbati. Our findings suggest that higher grain iron concentration of cv. Sharbati might be due to higher expression of key Fe transporters (viz. OsYSL2, OsYSL8 and OsITR1) and root membrane bound OsFRO1, which give an advantage in terms of absorption, transport and assimilation of Fe by this cultivar as compared to the low iron containing cultivar, Lalat.
2016-12-31 | GSE70093 | GEO
Project description:Grain length is a prominent determinant for the grain weight and appearance quality of rice. To elucidate the genetic basis of the control of grain length, we conducted quantitative trait locus (QTL) mapping to determine a genomic interval responsible for the a long-grain phenotype observed in a japonica cultivar HD385 by using an F2:3 population and recombinant inbred line (RIL) population, which is are derived from a cross between the long-grain japonica cultivar HD385 and short-grain japonica cultivar Nipponbare (NIP). This led to the identification of a novel QTL, which is located on chromosome 3, for grain length, named qIGL1 (for Increased Grain Length 1); the HD385-derived allele showed enhancement effects on grain length, and such an allele as well as NIP-derived allele are were thus designated qigl1 HD385 and qIGL1NIP, respectively. Genetic analysis revealed that qigl1HD385 displayed semi-dominant effects on grain length. To further narrow down the qIGL1 region, we developed a few advanced backcross populations to determine the precise location of qIGL1. Eventually, qIGL1 was delimited to a 70.8-kb region containing 9 open reading frames (ORFs). A comprehensive analysis indicated that ORF6 and ORF9, separately corresponding to LOC_Os03g30530 and LOC_Os03g30550, are were found to carry base substitutions and/or deletions, which resulted in changes or losses of amino acid residues. However, these alterations in coding sequences does did not significantly change the expression levels of both ORFs. To further elucidate the mechanisms behind the increases of grain length conferred by qigl1HD385, we generated a pair of near-isogenic lines (NILs), termed NIL-qigl1HD385 and NIL-qIGL1NIP, and discovered that introduction of qigl1HD385 into the NIP background significantly lead resulted into the elevations of grain length and 1000-grain weight. Closer inspection of outer epidermal cells of grain surfaces of both lines revealed that the cell length and width in the longitudinal direction are were significantly longer in NIL-qigl1HD385 compared with in NIL-qIGL1NIP, which may might stem partly from the downregulation of several cell cycle-related genes. Hence, our study studies identify identified a new semi-dominant natural allele contributing to the increase of grain length, and further shed light on the regulatory mechanisms of grain length.
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