The panicle architecture and grain size of rice affect not only grain yield but also grain quality, especially grain appearance. The erect-panicle (EP) trait controlled by the qpe9-1/dep1 allele has been widely used in high-yielding japonica rice breeding, but usually accompanied with moderate appearance of milled rice. The null gs9 allele shows a good potential for improving grain shape and appearance. However, GS9 and qPE9-1/DEP1 loci are tightly linked, and their interaction is unclear, which obviously restricts their utilization in modern rice breeding. In the present study, comparative analyses of protein and mRNA levels revealed that GS9 and qPE9-1 function independently. Three near-isogenic lines (NILs) carrying various allelic combinations of these two loci, NIL (gs9/qpe9-1), NIL (GS9/qPE9-1) and NIL (gs9/qPE9-1), in the EP japonica cultivar 2661 (GS9/qpe9-1) background were developed for genetic interaction analysis. GS9 and qPE9-1 had additive effects on determining grain size, and the null gs9 allele could decrease grain chalkiness and improve grain appearance without affecting plant and panicle architecture in EP japonica cultivars. Additionally, introgression lines (ILs) developed in another released EP japonica cultivar Wuyujing 27 (WYJ27) background showed the same additive effect and the feasibility of utilizing the gs9 allele to improve grain appearance quality in high-yielding EP cultivars. This study provides an effective strategy for rice breeders to improve rice grain appearance in EP japonica and related cultivars.

There are nearly 1 000 rice landrace varieties in the Taihu basin, China. To assess the genetic diversity of the rice, 24 intragenic molecular markers (representing 17 starch synthesis-related genes) were investigated in 115 Taihu basin rice landraces and 87 improved cultivars simultaneously. The results show that the average genetic diversity and polymorphism information content values of the landraces were higher than those of improved cultivars. In total, 41 and 39 allele combinations (of the 17 genes) were derived from the landraces and improved cultivars, respectively; only two identical allele combinations were found between the two rice variety sources. Cluster analysis, based on the molecular markers, revealed that the rice varieties could be subdivided into five groups and, within these, the japonica improved rice and japonica landrace rice varieties were in two separate groups. According to the quality reference criteria to classify the rice into grades, some of the landraces were found to perform well, in terms of starch quality. For example, according to NY/T595-2002 criteria from the Ministry of Agriculture of China, 25 and 33 landraces reached grade 1, in terms of their apparent amylose content and gel consistency. The varieties that had outstanding quality could be used as breeding materials for rice quality breeding programs in the future. Our study is useful for future applications, such as genetic diversity studies, the protection of rice variety and improvment of rice quality in breeding programs.

Eating and cooking qualities (ECQs) of rice are important attributes due to its major influence on consumer acceptability. To better understand the molecular mechanism of the variation in ECQs, we investigated and compared the expressions among different alleles of the Waxy (Wx) gene and its effect on ECQs in specialty rice cultivars. The results showed that the accumulation of amylose was positively and significantly correlated to the level of mature Wx mRNA and granule-bound starch synthase I (GBSS I) in developing rice grain at 12 days after flowering. The amount of GBSS I and its activity together are the main factors controlling amylose synthesis. Differences in ECQs among five Wx allele types were investigated in samples from 15 rice varieties. The apparent amylose content (AAC) and gel consistency (GC) were similar in each type of Wx allele. The AAC followed the order, Wxa type>Wxin type>Wxb type>Wxmq type>wx. Contrary to this, the GC showed an opposite trend compared to AAC. There was a wide variation in rapid visco analyzer (RVA) profile among five Wx allele types, while varieties sharing a specified Wx allele had basically the similar RVA profile, although there was a slight difference in some RVA parameters, peak, hot paste and cool paste viscosities.