Yield and quality are two important factors in rice breeding. With the improvement of people's living standards in China, the requirements for rice quality are increasing. Guangxi may be one of the origins of cultivated rice [25], with abundant wild rice and landrace resources, which provides a good material basis for the genetic improvement of rice varieties in Guangxi. Amylose content is an important food quality trait of rice. Generally, rice varieties with high amylose content have large rice swelling, poor rice stickiness and softness, easy to harden after cooling, and poor taste; the rice varieties with low amylose content are sticky, elastic, soft, and easier to digest; the rice varieties with medium amylose content show good stickiness and softness, and they are not sticky after cooling, and can maintain softness and palatability [45]. Before the 1990s, the amylose content of conventional rice approved in Guangxi was higher and then began to decrease, but the amylose content of the newly approved varieties increased. The amylose content of hybrid rice varieties has been on a downward trend. The average amylose content of conventional rice was compared with that of hybrid rice varieties, and the amylose content of conventional rice was generally lower. Another important rice cooking and eating quality parameter is alkali consumption value. The alkali consumption values of conventional rice varieties and hybrid rice varieties were significantly improved. The gel consistency of conventional rice is rapidly improved, while the gel consistency of hybrid rice is a relatively slow improvement process.
Appearance quality is the most intuitive quality trait, which consumers can distinguish with naked eyes, mainly including grain shape, chalkiness and transparency of rice, of which grain shape and chalkiness are the most important appearance quality traits. Compared with hybrid rice, the length/width ratio, chalkiness and chalky grain rate of conventional rice were generally better than those of hybrid rice, which may be related to the higher quality starting point of conventional rice. After 2000, the length/width ratio, as an important indicator of rice grading, played a role in promoting the development of rice appearance quality. This study found that the length/width ratio of early-bred hybrid rice materials was generally lower than 3.0, such as Zhenshan 97, Longtefu B and Bo B. With the increasing requirements of breeders for the appearance and quality of rice, the length/width ratio of some important maintainer lines exceeded 4.6, such as Lilac B. The length/width ratio of some important restorer lines exceeded 4.7, such as Gui 117, R Lisi, R Yousi, R Basi and R Simiao. The chalkiness and the chalky grain rate of conventional rice and hybrid rice have the same trend. Since 2000, the chalkiness and the chalky grain rate have gradually decreased. The chalkiness and the chalky grain rate of hybrid rice are highly coincident. For example, Yexiang B and Gui 117R have low chalkiness and chalky grain rate, while chalkiness and chalky grain rate were higher in Longtefu B, Yuehui 9802 and Zhenshan 97. The chalkiness of rice is opaque. The test results show that Yexiang B, Gui 117 and RYousi have higher transparency, and Longtefu B, Yuehui 9802 and Zhenshan 97 have lower transparency.
Rice milling quality mainly includes brown rice rate, milled rice rate and head rice rate. The brown rice rate of conventional rice did not increase significantly, while the head rice rate increased and decreased alternately. Both the brown rice rate and the head rice rate of hybrid rice tended to increase, especially the milled rice rate increased significantly. In general, the newly bred hybrid rice materials had a higher rate of head rice, but some early bred varieties Longtefu B and Gui 99 also had a high head rice rate.
Through the analysis of 38 genome-wide association and selected regions, we found that ALK, BG2, GL3.1, GL7/GW7, GPA3, GS3, OsMKKK10, Wx, An-1, BG1, CLG1, GS5, GW8 and RGG2 may be associated with related to the improvement of rice quality traits in Guangxi. Among them, ALK, GPA3 and Wx genes were related to rice cooking and eating quality. Based on the functional variation of ALK gene caused by SNP, there are at least three haplotypes of ALK, A-GC, G-TT and G-GC [46]. Before 2014, there were more varieties of GC genotype, and after that, breeders chose more varieties of TT genotype. Studies have shown that the Wx gene has 9 alleles, of which Wxa and Wxb are the two most important alleles, corresponding to high and low amylose content [1]. The results of Wx genotyping of 38 rice materials in this study showed that the early rice materials were mainly Wxa alleles, while the rice materials after 2011 were all Wxb alleles, indicating that breeders prefer materials with low amylose content. GPA3 is another rice quality-related gene identified in this study. Its mutant gpa3 has a significantly reduced grain filling rate, showing loose arrangement of starch granules in the endosperm and an opaque grain phenotype [33]. Therefore, breeders are more inclined to select for the GPA3 genotype.
In this study, we identified 11 genes related to rice appearance quality, including BG2, GL3.1, GL7/GW7, GS3, OsMKKK10, An-1, BG1, CLG1, GS5, GW8 and RGG2. GS3 is the major gene affecting grain shape [6]. The analysis of GS3 genotypes of 38 rice materials found that before 2007, the bred quality was mainly C genotype (short-grain shape), and after that, all bred varieties were A genotype (long-grain shape). GL7/GW7 is the major gene controlling grain length and grain width [31, 32]. The analysis shows that this gene was C genotype before 2015, and then the rice materials of T genotype began to increase, which may be related to this gene being cloned. GS5 is a quantitative trait gene that controls grain width, fullness, and thousand-grain weight in rice [39]. Before 2015, it was mainly C genotype, and after that, it was mainly T genotype. It can be seen from the above results that the improvement of rice grain shape is a gradual process. Furthermore, GW8 is able to directly bind to the GW7 promoter and inhibit its expression [31]. CLG1 encodes a ubiquitin ligase that targets and ubiquitinates the full-length form of the GS3 protein, and this modified GS3 is selected for entry into the endomembrane system, where it is degraded in the vacuole, balancing G protein signaling, and leading to grain enlargement [40]. At present, scientists have cloned many genes involved in the regulation of rice grain shape[1], which provides a wealth of genetic resources for breeders to improve the appearance and quality of rice.
Marker-assisted selection (MAS) is a new technology with the rapid development of modern molecular biology technology. The use of MAS methods to encapsulate the genetic composition of individual resistance allows the aggregation of multiple favorable genes from different sources in one cultivar [47]. At present, we designed functional markers for the functional variation sites of 7 genes: Wx, ALK, GS3, GL7/GW7, GS5, Chalk5 and fgr, and examined the genotypes of 38 rice materials. We found Gui 569, Gui 117, Gui 721, Gui 726, R Yousi, R Simiao and R Basi contained 7 superior alleles; Yexiang B and Lisi contained 6 superior alleles. CRISPR-Cas9 technology allows site-directed editing of target genes, which has important breeding value for the targeted breeding of specific traits of crops. At present, researchers use CRISPR/Cas9 technology to perform gene editing on Wx[48], GL7[49], fgr[49], etc., to improve rice quality. We used CRISPR/Cas9 technology to perform gene editing on the GS3 of Mei 1B to obtain a high-quality maintainer line Mei 2B, and finally obtained a high-quality sterile line Mei 2A by hybridization, backcrossing, and other methods [12].