Genetic editing of GS3 via CRISPR/Cas9 Accelerates the Breeding of Three-line Hybrid Rice With Superior Yield and Grain Quality

Abstract Grain size is one of the major traits that control rice grain yield and quality. The GS3 gene, a major QTL regulating grain length and weight, is the first one been identified. A mutation occurred in its N-terminal organ size regulating domain (OSR)results in a loss of function of the mutant allele gs3 and rice varieties carry this gs3 allele often produce longer grains. In this study, we exploited the CRISPR/Cas9 gene editing technology to introduce an edited gs3 allele, two guide RNAs(gRNA) targeted at the OSR of the GS3 gene were transformed into one of our indica maintainer lines, GM1B, for its grain yield and quality improvement. Through molecular analysis and sequencing, in T1 generation, a homologous edited-gs3 mutant line without tansgene was obtained and name as GM2B, then converted to CMS line GM1A by backcrossing to obtain another superior male sterile line GM2A for further tests. GM2B showed improved grain quality and yield compared to the WT GM1B, with grain length increased by 7.9%, length/width ratio increased from 3.89 to 4.19, TGW increased by 6.7%, and grain yield per plant increased by 14.9%. Meanwhile, genetic improvement of other quality traits including rice length (6.83mm), rice grain length/width ratio (3.61), matched the appearance standards set for traditional Simiao (silk seedling) type cultivars. Two restorer lines were outcrossed to both GM1A and GM2A to produce hybrid rice. Compared to GM1A’s two hybrids, the hybrids of GM2A had longer grains, higher length/width ratio, higher TGW and yield per plant. In addition, hybrids of GM2A showed better performance on grain appearance including better translucency, lower chalky rice rate and chalkiness degree than hybrids of GM1A.These data strongly demonstrate that the introduction of an elite gs3 allele into GM1A via CRISPR/Cas9 gene editing technology leads to significant genetic improvement. The resultant CMS line GM2A(gs3) performs much better than the original GM1A on grain quality and yield. Thus, our study proves that targeted genetic improvement using gene editing technology can expedite rice breeding, especially the breeding of three-line hybrid rice.

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Combined Linkage Mapping and Genome-Wide Association Study Identified QTLs Associated with Grain Shape and Weight in Rice (Oryza sativa L.)

Agronomy ◽

10.3390/agronomy10101532 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1532

Author(s):

Ju-Won Kang ◽

Nkulu Rolly Kabange ◽

Zarchi Phyo ◽

So-Yeon Park ◽

So-Myeong Lee ◽

...

Keyword(s):

Linkage Mapping ◽

Genome Wide Association Study ◽

Grain Shape ◽

Genome Wide Association ◽

Width Ratio ◽

Rice Grain ◽

Grain Length ◽

Transplanted Rice ◽

Genome Wide ◽

Length Width

In the current study, we used a linkage mapping–Genome-Wide Association Study (GWAS) joint strategy to investigate quantitative trait loci (QTLs) governing rice grain shape and weight in a doubled haploid (DH) population, using Kompetitive Allele-Specific PCR (KASP) markers. Results revealed the co-detection of the QTLs, qGLE-12-1 and qGLE-12-2 (Chromosome 12), qGTE-3-1 (Chromosome 3), and qGWL-5-1 and qLWRL-5-1 (Chromosome 5), associated with grain length, width, and length–width ratio, by both linkage mapping and GWAS. In addition, qGLL-7-1 (logarithm of the odds (LOD): 18.0, late-transplanted rice) and qGLE-3-1 (LOD: 8.1, early-transplanted rice), and qLWRL-7-1 (LOD: 34.5), detected only by linkage mapping, recorded a high phenotypic variation explained (PVE) of 32.5%, 19.3%, and 37.7% for grain length, and grain length–width ratio, respectively, contributed by the allele from 93-11. Meanwhile, qGWL-5-1 (LOD: 17.2) recorded a high PVE (31.7%) for grain width, and the allele from Milyang352 contributed to the observed phenotypic variation. Furthermore, qGTL-5-1 (LOD: 21.9) had a high PVE (23.3%) for grain thickness. Similarly, qTGWE-5-1 (LOD: 8.6) showed a high contribution to the PVE for grain weight (23.4%). Moreover, QTLs, qGW-5-1, qGT-5-1, qLWR-5-1, and qTGW-5-1 coincided on chromosome 5, flanked with KJ05_17 and KJ05_13 markers. Therefore, these QTLs are suggested to govern rice grain shape and weight. Additionally, the identified candidate genes could play active roles in the regulation of rice grain shape and weight, regarding their predicted functions, and similarity with previously reported genes. Downstream breeding and functional studies are required to elucidate the roles of these candidate genes in the regulation of grain shape and weight in rice.

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Evaluation of Traits Associated With Seed Characteristics in Arkansas Restorer Lines

10.21203/rs.3.rs-790450/v1 ◽

2021 ◽

Author(s):

Ozgur Azapoglu ◽

Vibha Srivast ◽

Xueyan Sha ◽

Ehsan Shakiba

Keyword(s):

Hybrid Rice ◽

Width Ratio ◽

Rice Grain ◽

University Of Arkansas ◽

Qtl Detection ◽

Seed Shape ◽

Seed Length ◽

Length Width ◽

Seed Width ◽

Seed Characteristics

Abstract Rice Grain dimension and weight are two critical factors for marketing and increasing yield capacity. Seed shape is measured by its length, width, thickness, and ratio of length-width. In this study, an experiment was conducted in a controlled condition from fall 2017 to 2020 to identify QTL and candidate genes associated with seed dimension and weight using a bi-parental population resulting from two University of Arkansas developed genotypes: a restorer line 367R and an advanced breeding line RU1501139, in Stuttgart, Arkansas. Five seed dimension traits, including seed length, seed width, seed thickness, seed length-width ratio, and 100-seeds weight, were obtained for QTL detection. The study detected a total of 17 QTL. Four QTL associated with seed length were identified, in which two were positioned on chr. 3, one on chr. 7, and one on chr. 11. Two QTL related to seed length-width ratio were detected on chr. 3 and 7. Whereas a total of three QTL were identified for seed thickness, one each on chr. 5, 6, and 8. Eight QTL associated with seed weight were found, of which four QTL were detected on chr. 12, two each on chr. 1 and 10, and one on chr. 3. Of 17 QTL, four QTL originated from RU1501139, while the origin of the other 13 QTL was 367R. Since multiple genes could control the yield and seed physical characteristics, the detected QTL can play a role in introducing superior parental lines for developing conventional and hybrid rice production.

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Physico-chemical attributes and correlation among grain quality traits of some exotic aromatic rice lines

Journal of the Bangladesh Agricultural University ◽

10.3329/jbau.v11i2.19899 ◽

2014 ◽

Vol 11 (2) ◽

pp. 227-232

Author(s):

S Seraj ◽

L Hassan ◽

SN Begum ◽

MM Sarker

Keyword(s):

Negative Correlation ◽

Grain Quality ◽

Positive Association ◽

Negative Association ◽

Width Ratio ◽

Quality Traits ◽

Grain Length ◽

Length Width ◽

Chemical Attributes ◽

Grain Width

Forty three rice genotypes were used to evaluate their aroma detection through sensory test. Aroma was detected by 1.7% KOH as a sensory test. Thirteen rice genotypes were detected having strong aroma; ten had moderate aroma; fifteen had slight aroma and five had no aroma. In case of grain shape study, 37 genotypes were evaluated as slender and six as medium. In this study, grain aroma had significant and positive association with grain length width ratio; significant and negative association with grain width, significant and negative association with gelatinization temperature, and significant and negative association with grain length. Gelatinization temperature had significant and negative correlation with grain length, significant and negative association with grain length width ratio, significant and positive association with grain width. Grain length had significant and negative correlation with grain width; significant and positive correlation with length width ratio. Grain width had significant and negative correlation with length width ratio. Finally, it can be concluded that among 43 genotypes Basmati370,CT19541-13-3-1-2P- 1P,PSBRC18,PSB-RC2(IR32809-26-3-3),IR64,IR50,2001059-TR2151-6-1-1,IR64-P401,IR72-P204 were found good grain quality traits having higher physico-chemical attributes. These elite lines could be readily used in breeding programmes to improve grain quality traits. DOI: http://dx.doi.org/10.3329/jbau.v11i2.19899 J. Bangladesh Agril. Univ. 11(2): 227-232, 2013

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Effects of Cultivar, Nitrogen Rate, and Planting Density on Rice-Grain Quality

Agronomy ◽

10.3390/agronomy8110246 ◽

2018 ◽

Vol 8 (11) ◽

pp. 246 ◽

Cited By ~ 8

Author(s):

Chanchan Zhou ◽

Yuancai Huang ◽

Baoyan Jia ◽

Yan Wang ◽

Yun Wang ◽

...

Keyword(s):

Grain Quality ◽

Amylose Content ◽

Brown Rice ◽

Planting Density ◽

Eating Quality ◽

Width Ratio ◽

Rice Grain ◽

Apparent Amylose Content ◽

Length Width ◽

Cooking And Eating Quality

To achieve superior rice-grain quality, more emphasis has been placed on the genetic diversity of breeding programs, although this improvement could be seriously restricted in the absence of comparable agricultural management practices. Nitrogen (N) application and planting density are two important agronomic practices influencing rice growth, yield, and grain quality. This study investigated the four main aspects of rice-grain quality, namely, milling (brown-rice, milled-rice, and head-rice percentage), appearance (length/width ratio, chalky-kernel percentage, and chalkiness), nutrition (protein content), and cooking and eating quality (apparent amylose content, gel consistency, and pasting viscosities) of two rice cultivars (Shendao 47 and Jingyou 586) under four N rates (0, 140, 180, and 220 kg ha−1), and three planting densities (25 × 104, 16.7 × 104, and 12.5 × 104 hills ha−1) in a field trial from 2015 to 2016. The four main aspects of rice-grain quality were significantly influenced by cultivar. Several aspects were affected by the interactions of N rate and cultivar. No significant interaction between N rate and plating density was detected for all grain-quality parameters. A higher N rate increased the percentages of brown rice and head rice, chalky-kernel percentage, and setback and peak time values, but reduced the length/width ratio, chalkiness, apparent amylose content, gel consistency, and peak-, trough-, and final-viscosity values. These results indicate that the N rate has a beneficial effect on milling and nutritional quality, but a detrimental effect on appearance and cooking and eating quality. Jingyou 586 and Shendao 47 had different responses to planting density in terms of grain quality. Our study indicates that low planting density for Jingyou 586, but a medium one for Shendao 47, is favorable for grain quality.

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Morphological Observation and Correlation of Growth and Yield Characteristics with Grain Quality and Antioxidant Activities in Exotic Rice Varieties of Afghanistan

Agriculture ◽

10.3390/agriculture9080167 ◽

2019 ◽

Vol 9 (8) ◽

pp. 167 ◽

Cited By ~ 4

Author(s):

Kifayatullah Kakar ◽

Tran Dang Xuan ◽

Saidajan Abdiani ◽

Imran Khan Wafa ◽

Zubair Noori ◽

...

Keyword(s):

Physicochemical Properties ◽

Grain Yield ◽

Grain Quality ◽

Antioxidant Activities ◽

Growth And Yield ◽

Yield Potential ◽

Morphological Observation ◽

Rice Grain ◽

Rice Varieties ◽

Panicle Number

Rice is an important staple food for Afghans. Its production has been increased, and attention is needed to improve grain quality. Experiments were conducted to evaluate the growth, yield, physicochemical properties, antioxidant activity, and morphological structures of four exotic rice varieties widely grown in Afghanistan (Attai-1, Jalalabad-14, Shishambagh-14, and Zodrass). Antioxidant activities, including 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS), of rice grain were determined. A scanning electron microscopic observation was conducted on the cross-cut section of dehulled rice grains. The results showed a wide variation among four rice varieties for growth, grain yield, physicochemical properties, antioxidant activities, and morphology. Tiller and panicle number per hill, 1000-grain weight, grain yield, and antioxidant activities were found to be highest in Jalalabad-14. Attai-1 showed lower amylose, protein, and lipid contents with a high number of perfect grains, consequently enhanced taste point (score of quality). Grain yield, protein, and amylose contents showed a negative correlation with antioxidant activities. Accumulated structures in Attai-1, Shishambagh-14, and Zodrass were normal; however, Jalalabad-14 increased protein bodies and its traces in the amyloplasts. Information on yield potential, grain quality, and nutritional value of these exotic rice varieties may useful for sustainable food provision and nutritional improvement of rice in Afghanistan.

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Variation in biological characteristics of purified pea ferritin (Fer) transgenic rice

Chinese Journal of Agricultural Biotechnology ◽

10.1017/s1479236207001672 ◽

2007 ◽

Vol 4 (3) ◽

pp. 213-219

Author(s):

Ye Hong-Xia ◽

Guo Ze-Jian ◽

Li Mei ◽

Xu Xiao-Hui ◽

Bao Jin-Song ◽

...

Keyword(s):

Transgenic Rice ◽

Iron Content ◽

Agronomic Traits ◽

Brown Planthopper ◽

Brown Rice ◽

Width Ratio ◽

Foreign Gene ◽

Rice Grain ◽

Milled Rice ◽

Grain Length

AbstractAfter seven generations of self-crossing assisted by β-glucuronidase (GUS) detection, 26 homozygous transgenic rice lines were obtained. Transgene effects on iron content, agronomic traits, rice quality and stress tolerance were studied. The results indicated that the average iron content in the milled grain of the transgenic (pea ferritin, Fer) rice (Oryza sativa) was 10.37 μg/g among all the homozygous lines, and only four lines (Fer34, Fer36, Fer39 and Fer65) had significantly higher iron contents than that of the control, Xiushui11 (6.46 μg/g). Significant differences in main agronomic traits, such as days from sowing to heading, plant height, main panicle length, total grains of main panicle, seed setting rate, 1000-grain weight, and yield per plant were observed among some homozygous lines, but similar flag leaf length and number of panicles per plant were found. This showed that insertion of the foreign gene (Fer) had a slight impact on the main agronomic traits, but that the transgene had no negative effects. The quality traits of homozygous rice lines, such as the percentage of brown rice, milled rice and full milled rice, grain length, grain width, ratio of grain length and width, and amylose content were all similar to those of the control. However, variations were noticed in chalkiness, translucency, alkali spreading value and gel consistency among partial homozygous lines. Responses of homozygous lines to low and high temperatures were not significantly correlated with the iron contents, and resistance to rice blast (Pyricularia oryzae), bacterial blight (Xanthomonas oryzae) and brown planthopper (Niaparvata lugens) were enhanced with increased iron contents.

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Identification and allele mining of new candidate genes underlying rice grain weight and grain shape by genome-wide association study

BMC Genomics ◽

10.1186/s12864-021-07901-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yanan Niu ◽

Tianxiao Chen ◽

Chunchao Wang ◽

Kai Chen ◽

Congcong Shen ◽

...

Keyword(s):

Grain Yield ◽

Association Study ◽

Candidate Genes ◽

Grain Quality ◽

Genome Wide Association Study ◽

Grain Shape ◽

Grain Weight ◽

Genome Wide Association ◽

Rice Grain ◽

Genome Wide

Abstract Background Grain weight and grain shape are important agronomic traits that affect the grain yield potential and grain quality of rice. Both grain weight and grain shape are controlled by multiple genes. The 3,000 Rice Genomes Project (3 K RGP) greatly facilitates the discovery of agriculturally important genetic variants and germplasm resources for grain weight and grain shape. Results Abundant natural variations and distinct phenotic differentiation among the subgroups in grain weight and grain shape were observed in a large population of 2,453 accessions from the 3 K RGP. A total of 21 stable quantitative trait nucleotides (QTNs) for the four traits were consistently identified in at least two of 3-year trials by genome-wide association study (GWAS), including six new QTNs (qTGW3.1, qTGW9, qTGW11, qGL4/qRLW4, qGL10, and qRLW1) for grain weight and grain shape. We further predicted seven candidate genes (Os03g0186600, Os09g0544400, Os11g0163600, Os04g0580700, Os10g0399700, Os10g0400100 and Os01g0171000) for the six new QTNs by high-density association and gene-based haplotype analyses. The favorable haplotypes of the seven candidate genes and five previously cloned genes in elite accessions with high TGW and RLW are also provided. Conclusions Our results deepen the understanding of the genetic basis of grain weight and grain shape in rice and provide valuable information for improving rice grain yield and grain quality through molecular breeding.

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Grain Yield in Indirect Selection for Multiple Characters in Upland Rice

Journal of Agricultural Science ◽

10.5539/jas.v11n2p516 ◽

2019 ◽

Vol 11 (2) ◽

pp. 516

Author(s):

Laís M. Tomé ◽

Flávia B. S. Botelho ◽

Douglas G. Castro ◽

Tácio P. da Silva ◽

Camila Soares Cardoso da Silva ◽

...

Keyword(s):

Grain Yield ◽

Upland Rice ◽

Block Design ◽

Good Alternative ◽

Width Ratio ◽

Leaf Blast ◽

Randomized Complete Block Design ◽

Length Width ◽

Selection For ◽

1000 Grain Weight

The aim of the present study was to compare the selection performed by the sum of standardized variables index (Z Index) with the selection based only on the grain yield character, to verify if the grain yield alone is a good alternative for the selection involving multiple characters. The experiments were conducted in Lavras-MG and in Lambari-MG, during the 2015/2016 agricultural year. The used design was the randomized complete block design with 3 replications. Thirty-six genotypes of the preliminary trial of upland rice breeding program of the Federal University of Lavras were evaluated. In order to compose the Z index, the following characteristics were evaluated: grain yield, height, number of days for flowering, 1000-grain weight, income, yield, leaf blast incidence, and grain length/width ratio. Z index was efficient in the selection for multiple characters whereas not all lines with the highest grain yield obtained good results in the other desirable characteristics, indicating that the selection based only on grain yield is not efficient when working with several characters of interest in upland rice cultivation.

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Genetic Diversity Relationship Between Grain Quality and Appearance in Rice

Frontiers in Plant Science ◽

10.3389/fpls.2021.708996 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hua Zhong ◽

Shuai Liu ◽

Gangqing Zhao ◽

Chenhao Zhang ◽

Zhaohua Peng ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Grain Quality ◽

Genome Wide Association Study ◽

Amylose Content ◽

Mixed Linear Model ◽

Grain Protein Content ◽

Width Ratio ◽

Rice Grain ◽

A Genome ◽

Trait Locus

Grain quality is an important breeding objective in rice, and the appearance of the grain also affects its commercial value in the market. The aim of this study was to decode the rice grain qualities and appearances, such as gelatinization temperature (GT), amylose content (AC), grain protein content (GPC), pericarp color (PC), length/width ratio (LWR), and grain volume (GV) at phenotypic and genetic levels, as well as the relationships among them. A genome-wide association study (GWAS) was used to identify the quantitative trait locus (QTLs) associated with the target traits using mixed linear model (MLM) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) methods. In general, AC was negatively correlated with GPC and GV, while it was positively correlated with LWR and PC. GPC was positively correlated with LWR. Using the rice diversity panel 1 (RDP1) population, we identified 11, 6, 2, 7, 11, and 6 QTLs associated with GT, AC, GPC, PC, LWR, and GV, respectively. Five germplasm lines, superior in grain qualities and appearances for basic breeding materials or improvement, were identified. Notably, an F-box gene OsFbox394 was located in the linkage disequilibrium (LD) block of qLWR7-2, which specifically expresses in endosperm and seed tissues, suggesting that this gene may regulate the seed development in rice grain. Besides, different haplotypes of OsHyPRP45 showed significant differences in AC, indicating that this gene may be related to AC in rice grain.

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EVALUATION OF NEW PROMISING RICE HYBRID AND ITS PARENTAL LINES FOR FLORAL, AGRONOMIC TRAITS AND GENETIC PURITY ASSESSMENT

The Pakistan Journal of Agricultural Sciences ◽

10.21162/pakjas/19.7297 ◽

2019 ◽

Vol 56 (03) ◽

pp. 567-576

Author(s):

Galal Anis

Keyword(s):

Grain Quality ◽

Seed Quality ◽

Hybrid Rice ◽

Agricultural Research ◽

Floral Traits ◽

Research Station ◽

Genetic Purity ◽

Cms Line ◽

Check Variety ◽

Parental Lines

Development of new rice hybrids with high-yielding and superior in grain quality is the most important goal to enhance food security as well as to achieve consumer requirements. High seed costs and poor grain quality are the major limiting factors for adoption of hybrid rice. A practical way to improve hybrid seed quality and to increase production is possible to increase the seed setting rate through improving the floral traits for parental lines. In the context, the study was conducted at the Rice Farm and Laboratories of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt in consecutive three rice growing seasons in 2015, 2016 and 2017. The study focused mainly on characterization of the new promising hybrid ‘G46A/GZ9399R’ and its parental lines. The cytoplasmic male sterile (CMS) line and restorer line were evaluated for twenty-three floral traits that influence outcrossing rate in hybrid rice under two seasons and there was a marked stability for most of these traits. As compared with commercial check variety ‘Giza 178’, the new promising hybrid ‘G46A/GZ9399R’ showed its superiority in all agro-morphological traits except plant height. This hybrid was very early, adapted widely and recorded 20.19% more yield than commercial check variety ‘Giza 178’. Instead, this hybrid produced superiority in all grain quality properties except grain length was medium grain and amylose content was equal for both studied genotypes compared to the check variety. In parallel, the assessment of genetic purity established the SSR markers RM154, RM331, and RM297, amplified alleles specific to differentiate parental lines of hybrid ‘G46A/GZ9399R’.

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