Research Progresses on QTLs for Main Grain Shape Genes in Rice

Mengxi ZHOU Diandong WANG Zhen’an BAI Ying PENG

Abstract The performance of rice quality affects the market competitiveness of rice to a certain extent, and grain shape is an important factor for yield traits and appearance quality. The mapping and cloning of major rice grain type genes were briefly reviewed, and the utilization of related genes in breeding was prospected.

Key words Rice; Rice grain quality; Grain size; Quantitative trait locus (QTL); Gene cloning

Received: July 27, 2021  Accepted: September 29, 2021

Mengxi ZHOU (1986-), female, P. R. China, assistant research fellow, master, devoted to research about rice quality analysis in molecular breeding.

*Corresponding author.

Rice is the main food crop in Asia. With the improvement of people’s lifestyle and consumption level, consumers have more and more demand for high-quality rice. Therefore, the improvement of rice quality has become a new trend to improve the competitiveness of the rice market. Appearance quality is an important index of rice quality. Rice grain shape trait is an important component of rice appearance quality and one of the important traits of rice yield. Therefore, research on the genetic and molecular mechanism of rice grain shape plays an important role in increasing rice yield and improving rice quality. In this paper, the related mapping and cloning research of main rice grain type genes was summarized, and the use of related genes in breeding was prospected, hoping to provide references for the research.

Inheritance of Rice Grain Shape

The grain shape of different rice varieties is quite different. Rice grain shape belongs to the inheritance of quantitative traits, controlled by polygenes, and is dominated by additive effects. It shows continuous variation in segregated populations, and the variation frequency often presents an overall distribution. Meanwhile, it shows cytoplasmic inheritance.

Regarding the inheritance of grain length, different studies have shown that grain length is co-controlled by single genes, double genes, polygenes, major genes and minor genes, and the inheritance of grain length is dominated by additive benefits. In recent years, domestic and foreign researches generally tend to acknowledge that rice grain length is controlled by polygenes. Regarding grain length, Rui  et al. ［1］ found that the inheritance of rice grain length was dominated by additive effects, with positive partial dominance, and nucleo-cytoplasmic interaction effects may exist.

Most studies have shown that the grain width in hybrid F2 populations shows a normal distribution and is controlled by the additive and dominant effects of polygenes. However, some studies have shown that the grain width of some varieties is controlled by single genes or major genes, their combinations of dominant genes are different, and there is a cytoplasmic effect in grain width. In addition, studies have shown that grain width is affected by maternity. Takite  et al. ［2］ found that among 28 combinations, the grain width of 18 combinations was partially dominant. And the wide grains of the F1 generations were partially dominant or non-dominant to narrow grains, and were only controlled by 1 to 4 pairs of genes.

Most studies believe that grain thickness is controlled by polygenes. Shi  et al. ［3］ found that the additive effect of rice grain thickness genes was obvious, with a narrow-sense heritability rate of 50.9%-95.0%. Rui  et al. ［1］ found that the inheritance of rice grain thickness was greatly affected by the environment, and the maternal effect was more significant.

The rice grain length-to-width ratio is affected by the two traits of grain length and grain width, and it is basically distributed as a whole in F2 populations. Xu  et al. ［4］ believe that the genetic expression of length-to-width ratio was dominated by maternal additive effects, which conformed to the additive-dominant model. Lin  et al. ［5］ showed that the length-to-width ratio of rice grains was mainly controlled by maternal inheritance, and the direct genetic effects and cytoplasmic genetic effects of seeds also had an impact on the length-to-width ratio.

QTL Mapping of Rice Grain Shape

Rice quality traits are mostly controlled by polygenes, and a large number of QTLs affecting quality traits have been mapped using parent-derived populations［6］. In the appearance quality of rice, grain type-related genes have received the most attention in the improvement of rice appearance quality. In-depth research on grain type-related genes can provide genetic resources and theoretical foundations for rice yield improvement and molecular breeding.

Rice grain type belongs to compound traits, including grain length, grain width and grain thickness, which are controlled by different major genes. So far, more than 400 QTLs controlling grain type have been found, all over the 12 chromosomes of rice. Most of them are distributed on chromosomes 2, 3, and 5. Among them, 103 are related to grain length, 95 are related to grain width, and 167 are related to grain weight, while few are related to grain thickness. Rabiei  et al. ［7］ located 5 QTLs related to grain length, including 1 major QTL, 7 QTLs related to grain width, 2 of which are major QTLs, and 6 QTLs related to length-to-width ratio, of which 2 are main-effect QTLs, and these main-effect QTLs all correspond to each other.

Study on Cloning and Function of Main QTLs for Rice Grain Shape

The cloning of grain shape genes helps to reveal the genetic mechanism of grain shape traits, and simultaneously provides a theoretical basis and technical basis for rice molecular marker-assisted breeding. In breeding practice, useful genes mainly include genes that control grain length traits: GS3, GL3.1/OsPPKL1, GW7/GL7,  etc. , genes that control grain width traits: GW2, GW5/qSW5, GS5,  etc. , and genes that control grain type: GS6, TGW6, GW8/OsSPL16, BG2, GW6a/Os-glHAT1, OsGRF4/GS2/GL2,  etc. ［8］.

Related genes controlling rice grain length

In terms of controlling grain length, GS3 located on chromosome 3 is the main QTL for grain weight and grain length. A large number of studies have shown that GS3 is the most important grain length regulator in cultivated rice natural populations and breeding populations, and has a negative regulatory effect on grain length［9］, and this mutation is widespread in global planting resources. The study by Mao  et al. ［10］ revealed the structural and functional characteristics of GS3 protein in regulating grain size, the OSR domain of its coding protein plays a negative role in regulating the length of grains, and the loss of ORS function can lead to the long grain phenotype.   In breeding practice, GS3 has been used to improve the grain length of rice. For example, Nan  et al. ［11］ updated the GS3 locus of Kongyu 131 to increase its grain length.

Another type that regulates grain length is  qGL3/OsPPKLI, GL3.1  and  qGL3-1 . qGL3 encodes protein phosphatase, and leads to long-grain phenotype through the conversion from aspartic acid to glutamic acid in the AVLDT motif. Gao  et al. ［12］ confirmed that the additive effects of  GS3  and  qGL3  on the regulation of rice grain length is greater than the genetic interaction effect, and the regulation of rice grain length by  qGL3  is greater than that of  GS3 . Qi  et al. ［13］ cloned and identified a new QTL that regulates rice grain length and yield:  GL3.1 . Functional analysis showed that the phosphorylation state of Cyclin-T1:3, a substrate that regulates GL3.1 protein, can control the division speed of glume cells, and then regulate grain size and yield. Hu  et al. ［14］ located  qGL3-1 , which affects rice grain length, in the 17 kb region of chromosome 3, with a single nucleotide substitution in the coding region of position 1 092 of exon 10.

GW7/GL7  are located at the same gene locus.  GW7  is a gene encoding TONNEAY 1. The up-regulation of this gene is related to the production of slender grains. The reason is that longitudinal cell division increases and horizontal cell division decreases. The  GL7  gene encodes a protein homologous to  Arabidopsis thaliana  LONGIFOLIA, and a tandem repeat of a 17.1 kb fragment at its locus leads to the up-regulation of GL7 and the down-regulation of its nearby negative regulatory factors, resulting in an increase in grain length and an improvement in appearance quality［15-16］.

Related genes controlling rice grain width

GW2 is a major QTL controlling rice grain width and grain weight, which encodes a circular E3 ubiquitin ligase. GW2 was found in the large-grain  Japonica  rice variety WY3 (Waiyin 3).   The lack of GW2 function leads to an increase in the number of cells, which makes the spikelet hull larger (wider), and accelerates the grain filling rate, thereby increasing the width, weight and yield of rice grains［17］. Choi  et al. ［18］ found that GW2 degraded the E3 ubiquitin ligase activity of EXPLA1 to negatively regulate grain size. Li  et al. ［19］ found that GW2 regulated the size of seeds through the direct interaction of proteins involved in carbohydrate metabolism.

Another major gene that regulates grain width and grain weight is  GW5/qSW5 , which is located on the short arm of chromosome 5. The physical location of the DNA sequence indicates that  GW5  and  qSW5  are the same gene. Liu  et al. ［20］ found that the GW5 protein is located on the plasma membrane and can physically interact with the kinase activity of rice GSK2 (glycogen synthase kinase 2) and inhibit its activity. It is also an effective gene control target for increasing the yield of rice and other food crops. Tian  et al. ［21］ discovered a homologue of GW5—GW5 (GW5L), which is similar in function to GW5 and is a negative regulator of rice grain size.

GS5 is a QTL that controls grain width, grain weight and seed setting rate. GS5 is located on chromosome 5 and is 2 Mb away from GW5/qSW5. It encodes a serine carboxypeptidase, which promotes cell division by up-regulating the expression of cell cycle genes, and regulates grain width by affecting cell size and number［22-23］. And GS5 has a higher expression level in young panicles, and positively controls rice grain width, fullness and 1 000-grain weight, and its high expression has larger grains.

Grain shape gene

GW8/OsSPL16 is a major QTL that controls grain width on the long arm of chromosome 8. It contains only one gene, which can positively regulate cell proliferation, and increasing the biomass of GW8 can promote cell division and filling［24］. GW8 affects grain width by regulating the number of glume cells, and affects grain size by regulating the expression of cell cycle-related genes. It is a transcription factor containing the SBP domain and can be directly combined with the promoter of grain length gene  GW7  to negatively regulate the expression of  GW7 ［22,25］.

Grain size is an important trait related to rice yield. Sun  et al. ［26］ identified and cloned an important gene  GS6  that negatively regulates rice grain size.  GS6  is a member of the  GRAS  gene family. Early termination of the coding sequence (CDS) at position 384 can significantly increase the grain width and weight of rice grains. Meanwhile, they identified the ggc repeat region encoding the  GRAS  domain in  GS6 .

GS2/GL2/OsGRF4 is located on chromosome 2. It is a transcriptional regulatory factor that encodes a GRF transcription factor containing QLO domain and WRC domain. GS2 mutation causes high expression of GS2/OsGRF4, which leads to cell enlargement and increase, thereby increasing grain weight and yield. OsGRF4 can interact with regulator GSK2 of the BR signaling pathway, and leads to the decrease of OsGRF4 activity, thereby specifically regulating the length of rice grains［27］.

TGW6 is the main QTL for controlling grain weight, which encodes the active protein of IAA glucose hydrolase, which can regulate the length of endosperm. The loss-of-function alleles increase grain weight through the regulation of source organs. Ishimaru  et al. ［28］ mapped it to a 4.9 kb fragment in 2013, and TGW6 has only one exon, and 6 nucleotide substitutions between the two mapped parents. TGW6 is expressed in sink-source organs, and is expressed at a high level in panicles, and TGW6 transcripts accumulate around endosperm pericarp. In terms of time, the highest expression level is 2 d after pollination and then gradually declines.

GIF1  encodes a cell wall invertase necessary for carbon metabolism at the early stage of grain filling. In cultivated rice, gene  GIF1  exhibits a restricted expression pattern during grain filling, and overexpression of  GIF1  can increase grain yield［29］. Wang  et al. ［30］ found that  GIF1  and  OsCIN1  are a pair of repetitive genes. The selection target of gene  GIF1  is the promoter region, while that of gene  OsCIN1  is the coding region.

Xu  et al. ［31］ found that BG2 regulated grain size by regulating the cell cycle process and promoted grain growth. It is highly expressed in seeds 5-8 d after pollination, it has great potential for rice breeding with the goal of increasing yield. BG2 is located on chromosome 7 and is identified as a giant embryo (GE) gene, which is essential for coordinating the balance between embryo and endosperm, and has the potential for popularization and application in  Indica  rice varieties［32］. Xu  et al. ［31］ also found that expressing CYP78A13 with a native promoter could also produce a large-grain phenotype, confirming that CYP78A13 can regulate spikelet hull development.

GW6 is a QTL that controls grain weight and is finely mapped to the 4.7 cM region. It plays a role by regulating transcription, and is capable of increasing the number of cells and accelerating grain filling, increasing spikelet hulls, and increasing grain weight and yield［33-34］. Li  et al. ［35］ introduced gene  GW6  into the  Indica  parent 9311 and the  Japonica  rice variety ZH11, and grain length, 1 000-grain weight and yield per plant after the improvement all increased.

Prospect

Rice quality is a comprehensive trait. At present, many rice quality-related regulatory genes have been located and cloned, and the function of the genes is relatively clear, which has laid a molecular foundation for improving rice quality, but only a few are actually used in breeding. There will be some problems in the process of improving the quality of rice. For example, the appearance quality of slender-grained rice will be improved, but the yield and the head rice rate will be reduced, while the wide-grain rice will increase chalkiness degree when increasing grain weight and yield. Therefore, in breeding practice, it is necessary to choose appearance quality and yield, and use different gene combinations to select specific grain types that increase yield, improve appearance quality, and increase product value. Meanwhile, specific good varieties can be selected according to different needs of different consumers for rice quality to achieve the optimal combination, meet different consumption needs and increase the commodity value of rice.  Although there are many basic researches on the improvement of rice quality traits, it is still necessary to further study the molecular mechanism of related genes and develop related molecular markers if they are to be applied in breeding practice. Improving rice quality through a single quality trait has certain limitations. It is also necessary to aggregate related high-quality genes into the same variety to improve the competitiveness of the variety. Furthermore, the use of gene editing and other technologies can also speed up quality improvement to a certain extent.

Mengxi ZHOU  et al.  Research Progresses on QTLs for Main Grain Shape Genes in Rice

References

［1］ RUI CQ, ZHAO AC. Diallel analysis of F1 genetic characteristics of grain weight and grain shape traits in  Indica  rice［J］. Scientia Agricultura Sinica, 2008(5): 14-20. (in Chinese)

［2］ GONG LH, GAO ZY, MA BJ,  et al.  Progress of genetic research on grain shape in rice［J］. Chinese Bulletin of Botany, 2011, 46(6): 597-605. (in Chinese)

［3］ SHI CH, SHEN ZT. Analysis of genetic effects of early  Indica  rice traits［J］. Journal of Zhejiang A & F University, 1994, 20(4): 405-410. (in Chinese)

［4］ LIN JR, WU MG, SHI CH. Analysis on genetic effects of appearance quality traits in  Japonica  hybrid rice［J］. Chinese Journal of Rice Science, 2001, 15(2): 93-96. (in Chinese)

［5］ XU CW, ZHANG AH, ZHU QS. Genetic analysis of quality traits in rice crosses between  Indica  and Japonica［J］. Acta Agronomica Sinica, 1996, 22(5): 530-534. (in Chinese)

［6］ QIU XJ, CHEN K, LV WK,  et al.  Examining two sets of introgression lines reveals background-independent and stably expressed QTL that inprove grain appearance quality in rice ( Oryza sativa  L.)［J］. Theoretical and applied genetics, 2017(130): 951-967.

［7］ RABIEI B, VALIZADEH M, GHAREYAZIE B,  et al.  Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers［J］. Euphytica, 2004(137): 325-332.

［8］ WANG H, ZHANG CH, CHEN JJ,  et al.  Research advances in the influence factors and related genes of rice quality traits［J］. China Rice, 2018, 24(4): 16-21. (in Chinese)

［9］ FAN CC, XING YZ, MAO HL,  et al.  GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein［J］. Theor appl genet, 2006(112): 1164-1171.

［10］ MAO HL, SUN SY, YAO JL,  et al.  Linking differential domain functions of the GS3 protein to natural variation of grain size in rice［J］. Proceedings of the national academy of sciences, 2010(107): 19579-19584.

［11］ NAN JZ, FENG XM, WANG C,  et al.  Improving rice grain length through updating the GS3 locus of an elite variety Kongyu 131［J］. Rice, 2018(11): 21.

［12］ GAO XY, ZHANG XJ, LAN HX,  et al.  The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons［J］. Bmc plant biology, 2015(15): 156.

［13］ QI P, LIN YS, SONG XJ,  et al.  The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3［J］. Cell research, 2012, 22(12): 1666-1680.

［14］ HU ZJ, HE HH, ZHANG SY,  et al.  A Kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice［J］. Journal of intergrative plant biology, 2012, 54(12): 979-990.

［15］ WANG SK, LI S, LIU Q,  et al.  The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality［J］. Nature genetics, 2015, 47(8): 949-954.

［16］ WANG YX, XIONG GS, HU J,  et al.  Copy number variation at the GL7 locus contributes to grain size diversity in rice［J］. Nature genetics, 2015, 47(8): 994-948.

［17］ SONG XJ, HUANG W, SHI M,  et al.  A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase［J］. Nature genetics, 2007, 39(5): 623-630.

［18］ CHOI BS, KIM YJ, MARKKANDAN K,  et al.  GW2 functions as an E3 ubiquitin ligase for rice expansin-like 1［J］. International journal of molecular sciences, 2018, 19(7): 1904.

［19］LEE KH, PARK SW, KIM YJ,  et al.  Grain width 2(GW2) and its interacting proteins regulate seed development in rice ( Oryza sativa  L.)［J］. Botanical studies, 2018, 59(1): 23.

［20］LIU JF,CHEN J, ZHENG XM,  et al.  GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice［J］.Nature climate change, 2017, 3(5): 951-957.

［21］ TIAN PT, LIU JF, MOU CL,  et al.  GW5-Like, a homolog of GW5, negatively regulates grain width, weight and salt resistance in rice［J］. Journal of integrative plant biology, 2019, 61(11): 1171-1185.

［22］ GONG R. The function study of rice OsGBP transcription factor family genes and the mapping and function analysis of the male and female gamete sterility gene MFS［D］. Guangzhou: South China Agricultural University, 2018. (in Chinese)

［23］ CHEN GW. QTL Mapping analysis of grain shape, grain weight and chalkiness rate in rice［D］. Guangzhou: South China Agricultural University, 2017. (in Chinese)

［24］ WANG SK, WU K, YUAN QB,  et al.  Control of grain size, shape and quality by OsSPL16 in rice［J］. Nature genetics, 2012, 44(8): 950-954.

［25］ WANG SK, LI S, LIU Q,  et al.  The OsSPL16-GW7 regulatory module determines grain shape and simultaneously inproves rice yield and grain quality［J］. Nature genetics, 2015b, 47(8): 949-954.

［26］ SUN KJ, LI XJ, FU YC,  et al.  GS6, a member of the GRAS gene family, negatively regulates grain size in rice［J］. Joumal of integrative plant biology, 2013, 55(10): 938-949.

［27］ CHE RH, Tong HN, SHI BH,  et al.  Control of grain size and rice yield by Gl2-mediated brassinosteroid responses［J］. Nature Plants, 2016, 2(1): 15195.

［28］ ISHIMARU K, HIROTSU N, MADOKA Y,  et al.  Loss of function of the IAA-glucose hydrolase gene  TGW6  enhances rice grain weight and increases yield［J］. Nature Genetics, 2013, 45(6): 707-711.

［29］ WANG ET, WANG JJ, ZHU XD,  et al.  Control of rice grain-filling and yield by a gene with a potential signature of domestication［J］. Nature genetics, 2008, 40(11): 1370-1374.

［30］WANG ET, XU X, ZHANG L,  et al.  Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication［J］. Bmc evolutionary biology, 2010(10): 108.

［31］ XU F, FANG J, OU SJ,  et al.  Variations in CYP78A13 coding region influence grain size and yield in rice［J］. Plant, cell & environment, 2015, 38(4): 800-811.

［32］ NAGASAWA N, HIBARA K, HEPPARD EP,  et al.  GIANT EMBRYO encodes CYP78A13, required for proper size balance between embryo and endosperm in rice［J］.The Plant Journal, 2013, 75(4): 592-605.

［33］ Guo LB, MA LL, JIANG H,  et al.  Genetic analysis and fine mapping of two genes for grain shape and weight in rice［J］. Journal of integrative plant biology, 2009, 51(1): 45-51.

［34］ SONG XJ, KUROHA T, AYANO M,  et al.  Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice［J］. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(1): 76-81.

［35］ LI YY, TAO HJ, ZHAO XQ,  et al.  Molecular improvement of grain weight and yield in rice by using  GW6  gene［J］. Rice science, 2014, 21(3): 127-132.