Genome-Wide Association Studies Reveal New Genetic Targets for Five Panicle Traits of International Rice Varieties

Narrow genetic background is a key limiting factor in breeding stable high-yielding rice. The introduction and utilization of international rice core germplasm is an important way to increase the genetic diversity of domestic rice varieties. We conducted a genome-wide association study on 5 panicle traits of 315 rice accessions introduced from the international rice micro-core germplasm bank. Based on the tests from Yangzhou of China and Arkansas of American, environment exhibited a significant impacts on panicle length and primary branch number, while grain length, grain width and grain length/width ratio were insensitive to environment changes. We discovered a total of 7, 5, 10, 8 and 6 chromosomal regions or single nucleotide polymorphism marker loci that were significantly associated with primary branch number, panicle length, grain length, grain width and grain length/width ratio, respectively. Among them, eleven regions were associated with grain shape and one region associated with primary branch number, showing the good consistence in two different environments. Significant linear correlation was discovered between the average trait value and the number of favorable alleles carried by the varieties in all associated loci. Among the associated loci, varieties in aromatic and tropical japonica sub-groups possessed most favorable alleles, while those in temperate japonica sub-group contained the least. The domestic varieties mainly harbored unfavorable alleles in six of the associated loci being detected. On the contrary, 15 varieties from 11 different countries harbored more favorable alleles （as many as 30 or more） than the others. Remarkably, all these 15 varieties belonged to the tropical japonica sub-group. In conclusion, our study demonstrates that varieties in the tropical japonica sub-group had high potentials for breeding stable high-yielding rice. Based on this discovery, we proposed a new approach for improving the panicle traits of domestic rice by using tropical japonica varieties.

QTLs analysis of rice peduncle vascular bundle and panicle traits

The vascular bundle in plants plays an important role intransportation of photosynthetic products, mineral nutri-ents, water, arid so on. Significant positive correlationswere found between grain yield, panicle traits and the No.of peduncle vascular bundles. So, it is very important tostudy the inheritance of peduncle vascular bundle, whichis a quantitative trait.

An integrated rice panicle phenotyping method based on X-ray and RGB scanning and deep learning

Rice panicle phenotyping is required in rice breeding for high yield and grain quality.To fully evaluate spikelet and kernel traits without threshing and hulling,using X-ray and RGB scanning,we developed an integrated rice panicle phenotyping system and a corresponding image analysis pipeline.We compared five methods of counting spikelets and found that Faster R-CNN achieved high accuracy(R~2 of 0.99)and speed.Faster R-CNN was also applied to indica and japonica classification and achieved 91%accuracy.The proposed integrated panicle phenotyping method offers benefit for rice functional genetics and breeding.

OsGRF4 controls grain shape, panicle length and seed shattering in rice

Traits such as grain shape, panicle length and seed shattering, play important roles in grain yield and harvest. In this study, the cloning and functional analysis of PANICLE TRAITS 2 （PT2）, a novel gene from the Indica rice Chuandali （CDL）, is reported. PT2 is synonymous with Growth-Regulating Factor 4 （OsGRF4）, which encodes a growth-regulating factor that positively regulates grain shape and panicle length and negatively regulates seed shattering. Higher expression of OsGRF4 is correlated with larger grain, longer panicle and lower seed shattering. A unique OsGRF4 mutation, which occurs at the OsmiRNA396 target site of OsGRF4, seems to be associated with high levels of OsGRF4 expression, and results in phenotypic difference. Further research showed that OsGRF4 regulated two cytokinin dehydrogenase precursor genes （CKX5 and CKX1） resulting in increased cytokinin levels, which might affect the panicle traits. High storage capacity and moderate seed shattering of OsGRF4 may be useful in high-yield breeding and mechanized harvesting of rice. Our findings provide additional insight into the molecular basis of panicle growth.

Novel pleiotropic loci controlling panicle architecture across environments in japonica rice (Oryza sativa L.)

To identify quantitative trait loci （QTLs） controlling panicle architecture in japonica rice, a genetic map was constructed based on simple sequence repeat （SSR） markers and 254 recombinant inbred lines （RILs） derived from a cross between cultivars Xiushui 79 and C Ban. Seven panicle traits were investigated under three environments. Single marker analysis indicated that a total of 27 SSR markers were highly associated with panicle traits in all the three environments. Percentage of phenotypic variation explained by single locus varied from 2% to 35%. Based on the mixed linear model, a total of 40 additive QTLs for seven panicle traits were detected by composite interval mapping, explaining 1.2%--35% ofphenotypic variation. Among the 9 QTLs with more than 10% of explained phenotypic variation, two QTLs were for the number of primary branches per panicle （NPB）, two for panicle length （PL）, two for spikelet density （SD）, one for the number of secondary branches per panicle （NSB）, one for secondary branch distribution density （SBD）, and one for the num- ber of spikelets per panicle （NS）, respectively, qPLSD-9-1 and qPLSD-9-2 were novel pleiotropic loci, showing effects on PL and SD simultaneously, qPLSD-9-1 explained 34.7% of the phenotypic variation for PL and 25.4% of the phenotypic variation for SD, respec- tively, qPLSD-9-2 explained 34.9% and 24.4% of the phenotypic variation for PL and SD, respectively. The C Bao alleles at the both QTLs showed positive effects on PL, and the Xiushui 79 alleles at the both QTLs showed positive effects on SD. Genetic variation of panicle traits are mainly attributed to additive effects. QTLx environment interactions were not significant for additive QTLs and additive x additive QTL pairs.