scholarly journals The identification of grain size genes by RapMap reveals directional selection during rice domestication

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Juncheng Zhang ◽  
Dejian Zhang ◽  
Yawei Fan ◽  
Cuicui Li ◽  
Pengkun Xu ◽  
...  
Keyword(s):  
Grain Size ◽  
Germplasm Collection ◽  
Directional Selection ◽  
Rice Grain ◽  
Isogenic Line ◽  
Shape Variation ◽  
Genomic Breeding ◽  
Simultaneous Integration ◽  
Trait Locus ◽  
Rice Domestication

AbstractCloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. Here, we introduce RapMap, a method for rapid multi-QTL mapping by employing F2 gradient populations (F2GPs) constructed by minor-phenotypic-difference accessions. The co-segregation standard of the single-locus genetic models ensures simultaneous integration of a three-in-one framework in RapMap i.e. detecting a real QTL, confirming its effect, and obtaining its near-isogenic line-like line (NIL-LL). We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. These genes explain a total of 75% of grain shape variation. Allele frequency analysis of these genes using a large germplasm collection reveals directional selection of the slender and long grains in indica rice domestication. In addition, major grain-size genes have been strongly selected during rice domestication. We think application of RapMap in crops will accelerate gene discovery and genomic breeding.

scholarly journals Differentially directional selection on grain size genes identified by RapMap during rice domestication

2020 ◽  
Author(s):  
Yibo Li ◽  
Juncheng Zhang ◽  
Dejian Zhang ◽  
Yawei Fan ◽  
Cuicui Li ◽  
...  
Keyword(s):  
Grain Size ◽  
Population Level ◽  
Isogenic Line ◽  
Molecular Architecture ◽  
Mini Core Collection ◽  
Trait Locus ◽  
Grain Size And Shape ◽  
Selection Intensities ◽  
Genetic Contributions ◽  
Rice Domestication

Abstract The ability to identify quantitative trait locus (QTL) genes controlling natural variation of important traits would facilitate the construction of a bridge between gene function analyses and domestication investigations. Grain size in rice is an important yield, quality and domestication trait. The molecular architecture and domestication signatures of grain size at population level remain unknown. Here we first introduce RapMap, a method for rapid and high-throughput QTL mapping employing a series of F2 gradient populations (F2GPs) constructed by trait-adjacent accessions from diverse germplasms. A co-segregation standard is set for simultaneously integrating the three-in-one framework in RapMap: detecting a real QTL, confirming its effect and obtaining its near-isogenic line-like line (NIL-LL), which greatly enhances the efficiency and robustness of QTL identification. Using 15 gradient populations, eight genes including two novel genes (GL1 and GW5.1) with different effects for grain size in rice were simultaneously discovered by RapMap in three years, which make more than two thirds of genetic contributions to grain size and shape in a mini-core collection worldwide. In-depth analyses of the eight genes employing a large and geographically diverse population, including 446 wild, 2462 landrace and 784 cultivar accessions, revealed that directional artificial selection of slender- and long- grains and their alleles played an important role during indica rice domestication. The genetic effects of the eight grain-size genes positively correlate with the differential selection intensities and the nucleotide variation intensities. Major grain-size genes fixed before the completion of rice domestication have been heavily selected for human requirements and cultivation practices. Generalizable application of the method and mimicking of the domestication nature will accelerate breeding modern cultivars.

scholarly journals A quantitative trait locus GW6 controls rice grain size and yield through the gibberellin pathway

2020 ◽  
Vol 103 (3) ◽  
pp. 1174-1188 ◽  
Author(s):  
Chuan‐Lin Shi ◽  
Nai‐Qian Dong ◽  
Tao Guo ◽  
Wang‐Wei Ye ◽  
Jun‐Xiang Shan ◽  
...  
Keyword(s):  
Grain Size ◽  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Rice Grain ◽  
Trait Locus

scholarly journals Dissection of Two QTL for Grain Size Linked on the Long Arm of Chromosome 5 in Rice

2021 ◽  
Author(s):  
xiaojun Niu ◽  
Zhenhua Zhang ◽  
Aye Nyein Chan ◽  
Yeyang Fan ◽  
Shaoqing Tang ◽  
...  
Keyword(s):  
Grain Size ◽  
Complex Traits ◽  
Grain Weight ◽  
Isogenic Line ◽  
Nucleotide Polymorphisms ◽  
Appearance Quality ◽  
Trait Locus ◽  
Significant Expression ◽  
Agronomical Traits ◽  
Previous Identification

Abstract Background: Most agronomical traits of crops are complex traits controlled by several major quantitative trait locus (QTL) and many minor QTL. Grain size determines grain weight and influences rice appearance quality. Identification of minor QTL is important for understanding the genetic and molecular network regulating grain size in rice. Following previous identification of QTL for grain weight and size using populations derived from the Teqing/IRBB52 indica rice cross, one QTL, qTGW5/qGL5 having significant effects on grain weight and length, was targeted for validation, dissection and fine-mapping.Result: Firstly, the effect of qTGW5/qGL5 was validated using two near isogenic line (NIL) F2 populations. Then, qTGW5/qGL5 was dissected into two closely linked QTL for grain size using four sets of NILs with sequential segregating regions. One of them, qTGW5 with the IRBB52 alleles increased grain weight, length and width with the same allelic direction, was located within an 1896.4-kb region flanked by RM18865 and Fi25273. The other one, qGL5 controlling grain length, was further delimited into a 68.8-kb region using seven NIL-F2 populations. Six annotated genes were found in the qGL5 region, of which five showed nucleotide polymorphisms between the two parental lines. In three of the six annotated genes, significant expression differences were detected between qGL5-NILs.Conclusions: Two closely-linked QTL having small effects for grain size in rice were separated using NIL-derived populations. One of them, qGL5 was fine-mapped into a 68.8-kb region containing six annotated genes. Our work lays a foundation for cloning minor QTL for grain size and offers potential targets for marker-assisted breeding in rice.

scholarly journals Verification and dissection of one quantitative trait locus for grain size and weight on chromosome 1 in rice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi-chen Cheng ◽  
Guan Li ◽  
Man Yin ◽  
Tosin Victor Adegoke ◽  
Yi-feng Wang ◽  
...  
Keyword(s):  
Grain Size ◽  
Quantitative Trait ◽  
Genetic Background ◽  
Molecular Design ◽  
Chromosome 1 ◽  
Recurrent Parent ◽  
Isogenic Line ◽  
Growing Seasons ◽  
Ril Population ◽  
Trait Locus

AbstractGrain size and weight are the key traits determining rice quality and yield and are mainly controlled by quantitative trait loci (QTL). In this study, one minor QTL that was previously mapped in the marker interval of JD1009-JD1019 using the Huanghuazhan/Jizi1560 (HHZ/JZ1560) recombinant inbred line (RIL) population, qTGW1-2, was validated to regulate grain size and weight across four rice-growing seasons using twenty-one near isogenic line (NIL)-F2 populations. The twenty-one populations were in two types of genetic background that were derived from the same parents HHZ and JZ1560. Twelve F9, F10 or F11 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were developed from one residual heterozygote (RH) in the HHZ/JZ1560 RIL population, and the remaining nine BC3F3, BC3F4 or BC3F5 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were constructed through consecutive backcrosses to the recurrent parent HHZ followed with marker assistant selection in each generation. Based on the QTL analysis of these genetic populations, qTGW1-2 was successfully confirmed to control grain length, width and weight and further dissected into two QTLs, qTGW1-2a and qTGW1-2b, which were respectively narrowed down to the marker intervals of JD1139-JD1127 (~ 978.2-kb) and JD1121-JD1102 (~ 54.8-kb). Furthermore, the two types of NIL-F2 populations were proved to be able to decrease the genetic background noise and increase the detection power of minor QTL. These results provided an important basis for further map-based cloning and molecular design breeding with the two QTLs in rice.

scholarly journals The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3

Cell Research ◽  
2012 ◽  
Vol 22 (12) ◽  
pp. 1666-1680 ◽  
Author(s):  
Peng Qi ◽  
You-Shun Lin ◽  
Xian-Jun Song ◽  
Jin-Bo Shen ◽  
Wei Huang ◽  
...  
Keyword(s):  
Grain Size ◽  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Rice Grain ◽  
The Novel ◽  
Trait Locus

scholarly journals A novel rice grain size gene OsSNB was identified by genome-wide association study in natural population

PLoS Genetics ◽  
2019 ◽  
Vol 15 (5) ◽  
pp. e1008191 ◽  
Author(s):  
Xiaosong Ma ◽  
Fangjun Feng ◽  
Yu Zhang ◽  
Ibrahim Eid Elesawi ◽  
Kai Xu ◽  
...  
Keyword(s):  
Grain Size ◽  
Association Study ◽  
Natural Population ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Rice Grain ◽  
Genome Wide

scholarly journals The Rho-family GTPase OsRac1 controls rice grain size and yield by regulating cell division

2019 ◽  
Vol 116 (32) ◽  
pp. 16121-16126 ◽  
Author(s):  
Ying Zhang ◽  
Yan Xiong ◽  
Renyi Liu ◽  
Hong-Wei Xue ◽  
Zhenbiao Yang
Keyword(s):  
Grain Size ◽  
Cell Division ◽  
Grain Yield ◽  
Molecular Mechanisms ◽  
Grain Filling ◽  
High Yield ◽  
Rice Grain ◽  
Rop Gtpase ◽  
Key Factor ◽  
Grain Width

Grain size is a key factor for determining grain yield in crops and is a target trait for both domestication and breeding, yet the mechanisms underlying the regulation of grain size are largely unclear. Here we show that the grain size and yield of rice (Oryza sativa) is positively regulated by ROP GTPase (Rho-like GTPase from plants), a versatile molecular switch modulating plant growth, development, and responses to the environment. Overexpression of rice OsRac1ROP not only increases cell numbers, resulting in a larger spikelet hull, but also accelerates grain filling rate, causing greater grain width and weight. As a result, OsRac1 overexpression improves grain yield in O. sativa by nearly 16%. In contrast, down-regulation or deletion of OsRac1 causes the opposite effects. RNA-seq and cell cycle analyses suggest that OsRac1 promotes cell division. Interestingly, OsRac1 interacts with and regulates the phosphorylation level of OsMAPK6, which is known to regulate cell division and grain size in rice. Thus, our findings suggest OsRac1 modulates rice grain size and yield by influencing cell division. This study provides insights into the molecular mechanisms underlying the control of rice grain size and suggests that OsRac1 could serve as a potential target gene for breeding high-yield crops.

scholarly journals Mechanical and Processing Properties of Rice Grains

2020 ◽  
Vol 12 (2) ◽  
pp. 552 ◽  
Author(s):  
Weronika Kruszelnicka ◽  
Andrzej Marczuk ◽  
Robert Kasner ◽  
Patrycja Bałdowska-Witos ◽  
Katarzyna Piotrowska ◽  
...  
Keyword(s):  
Grain Size ◽  
Oryza Sativa ◽  
Negative Correlation ◽  
Oryza Sativa L ◽  
Strength Properties ◽  
Rice Grain ◽  
Static Compression ◽  
Positive Correlation ◽  
Rice Grains ◽  
Processing Properties

Strength properties of grains have a significant impact on the energy demand of grinding mills. This paper presents the results of tests of strength and energy needed the for destruction of rice grains. The research aim was to experimentally determine mechanical and processing properties of the rice grains. The research problem was formulated in the form of questions: (1) what force and energy are needed to induce a rupture of rice grain of the Oryza sativa L. of long-grain variety? (2) what is the relationship between grain size and strength parameters and the energy of grinding rice grain of the species Oryza sativa L. long-grain variety? In order to find the answer to the problems posed, a static compression test of rice grains was done. The results indicate that the average forces needed to crush rice grain are 174.99 kg m·s−2, and the average energy is 28.03 mJ. There was no statistically significant relationship between the grain volume calculated based on the volumetric mass density Vρ and the crushing energy, nor between the volume Vρ and other strength properties of rice grains. In the case of Vs, a low negative correlation between strength σmin and a low positive correlation between the power inducing the first crack were found for the grain size related volume. A low negative correlation between the grain thickness a3, stresses σmin and work WFmax was found as well as a low positive correlation between thickness a3 and the force inducing the first crack Fmin.

Novel OsGRAS19 mutant, D26, positively regulates grain shape in rice (Oryza sativa)

2019 ◽  
Vol 46 (9) ◽  
pp. 857 ◽  
Author(s):  
Zhimin Lin ◽  
Jingwan Yan ◽  
Jun Su ◽  
Huaqing Liu ◽  
Changquan Hu ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Grain Size ◽  
Transcription Factor ◽  
Grain Shape ◽  
Rice Yield ◽  
Reproductive Development ◽  
Cell Number ◽  
Rice Grain ◽  
Regulatory Effect ◽  
Site Mutation

Grain size is an important factor in rice yield. Several genes related to grain size have been reported, but most of them are determined by quantitative trail loci (QTL) traits. Gene D26 is a novel site mutation of OsGRAS19 and involved in the brassinosteroid (BR) signalling pathway. However, whether D26 is involved in the process of rice reproductive development remains unclear. Here, gene cloning and functional analysis revealed that D26 has an obvious regulatory effect on grain size. Overexpression or CRISP/Cas9 mutant of D26 also showed that grain size was positively influenced. Cellular analyses show that D26 modulates grain size by promoting cell division and regulating the cell number in the upper epidermis of the glume. The overexpression results further suggest that the level of D26 expression positively impacts grain length and leaf angles and that the expression of several known grain size genes is involved in the regulation. Based on our results, D26, as a transcription factor, effectively improves rice grain shape.

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