Validation of the Red Pericarp Gene from 419 Rice Landraces in Guangxi via Genome-wide Association Studies

Rice has different colors of pericarp, such as red, white and black. Red rice pericarp is rich in proanthocyanins, which have antioxidant properties and are beneficial to human health. In the present study, we analyzed the red-pericarp gene Rc of 419 rice landraces in Guangxi by genome-wide association study （GWAS）, and validated that the Rc gene regulated the red periearp trait in flee. By analyzing the genomie DNA of 97 red-pericarp flee eultivars, we identified two new alleles in C139 and C323. Then, the exons of Rcc＇9 and Rcc were sequenced with Sanger method, and the results demonstrated that the natural mutations within Re ene resulted in the two alleles Rcc and Rcc.

OsNPF3.1,a member of the NRT1/PTR family,increases nitrogen use efficiency and biomass production in rice

The overuse of nitrogen(N)fertilizer in fields has increased production costs and raised environmental concerns.Increasing the N use efficiency(NUE)of rice varieties is crucial for sustainable agriculture.Here we report the cloning and characterization of OsNPF3.1,a gene that controls rice NUE.An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice.OsNPF3.1,which is expressed mainly in the aerial parts of rice,also affects rice plant height,heading date,and thousand-grain weight.The OsNPF3.1 protein is located in the plasma membrane.When OsNPF3.1 was subjected to artificial selection,two naturally varying loci were associated with NUE,of which OsNPF3.1Chr6_8741040differed between indica and japonica rice.OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE.

Transcriptome analysis reveals potential genes associated with plant height in rice

Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identified and described.Nonetheless,the molecular mechanism of height regulation in high-culm rice mutants has not been well studied.By using transcriptome and weighted gene co-expression network analysis(WGCNA),we identified the differentially expressed genes(DEGs)between high-culm rice mutants(MUT)and wild-type(WT)and explored the key pathways and potential candidate genes involved in PH regulation.Transcriptome analysis identified a total of 2,184 DEGs,of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage.Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction,ABC transportation,and steroid hormone biosynthesis.Among these metabolic pathways,LOC_Os05g43910 and LOC_Os01g35030 were auxin(IAA)-related genes,up-regulated in MUT and LOC_Os02g08500(LEPTO1),LOC_Os11g04720,and LOC_Os12g04500 were cytokinin(CK)-related genes,downregulated in MUT.The WGCNA identified four modules(light cyan,dark grey,grey,and pale turquoise)closely related to PH,and seven key genes were screened from these modules,of which two were up-regulated cell wallrelated genes(LOC_Os01g26174(OsWAK5),LOC_Os06g05050)in MUT,and one gibberellic acid(GA)gene(LOC_Os06g37364,OsKO2)was also up-regulated.These genes might be closely related to PH regulation.These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.

Functional metabolomics reveal the role of AHR/GPR35 mediated kynurenic acid gradient sensing in chemotherapy-induced intestinal damage

Intestinal toxicity induced by chemotherapeutics has become an important reason for the interruption of therapy and withdrawal of approved agents. In this study, we demonstrated that chemotherapeutics-induced intestinal damage were commonly characterized by the sharp upregulation of tryptophan(Trp)àkynurenine(KYN)àkynurenic acid(KA) axis metabolism. Mechanistically,chemotherapy-induced intestinal damage triggered the formation of an interleukin-6(IL-6)àindoleamine2,3-dioxygenase 1(IDO1)àaryl hydrocarbon receptor(AHR) positive feedback loop, which accelerated kynurenine pathway metabolism in gut. Besides, AHR and G protein-coupled receptor 35(GPR35) negative feedback regulates intestinal damage and inflammation to maintain intestinal integrity and homeostasis through gradually sensing kynurenic acid level in gut and macrophage, respectively. Moreover, based on virtual screening and biological verification, vardenafil and linagliptin as GPR35 and AHR agonists respectively were discovered from 2388 approved drugs. Importantly, the results that vardenafil and linagliptin significantly alleviated chemotherapy-induced intestinal toxicity in vivo suggests that chemotherapeutics combined with the two could be a promising therapeutic strategy for cancer patients in clinic.This work highlights GPR35 and AHR as the guardian of kynurenine pathway metabolism and core component of defense responses against intestinal damage.

水稻耐寒基因CTB4a的核苷酸多样性及区域适应性

为探究CTB4a基因的自然变异是否与栽培稻苗期耐低温相关,本研究以133份栽培稻(Oryza sativa L.)及35份普通野生稻(O.rufipogon Griff.)为实验材料,对CTB4a编码区的核苷酸多样性及其单倍型与地理分布的关系进行分析。结果表明CTB4a基因编码区有14个核苷酸变异,组成33个单倍型。Network分析发现,这些单倍型的286 bp处的SNP变异(+2,035,097 bp,G>C;+96 aa,Ala→Pro)将其分成Group A和Group B两组。Group A(CTB4a^(jap))共有56份样品,其中有43份(76.79%)是种植于中高纬度地区的粳稻;Group B(CTB4a^(ind))有77份样品,有63份(83.12%)是种植于热带和亚热带国家的籼稻。Group A中样品苗期黄叶率的平均值比Group B样品低30%,且两者耐寒性具有显著差异(P=1.25e-09)。位于286 bp处的变异只在Group A中出现,在Group B中均不存在,说明随着水稻种植区域向北迁移的育种过程中,栽培稻中出现了CTB4a^(jap)并被固定下来。该研究为理解水稻对低温适应的分子遗传机制和培育耐寒品种提供了理论基础。

Genetic dissection of top three leaf traits in rice using progenies from a japonica × indica cross

The size of the top three leaves of rice plants is strongly associated with yield; thus, it is important to consider quantitative traits representing leaf size （e.g., length and width） when breeding novel rice varieties. It is challenging to measure such traits on a large scale in the field, and little is known about the genetic factors that determine the size of the top three leaves. In the present study, a population of recombinant inbred lines （RILs） and reciprocal single chromosomal segment substitution lines （SSSLs） derived from the progeny of a japonica Asominori x indica IR24 cross were grown under four diverse environmental conditions. Six morphological traits associated with leaf size were measured,namely length and width of the flag, second and third leaves. In the RIL population, 49 QTLs were identified that clustered in 30 genomic region. Twenty-three of these QTLs were confirmed in the SSSL population. A comparison with previously reported genes/QTLs revealed eight novel genomic regions that contained uncharacterized ORFs associated with leaf size. The QTLs identified in this study can be used for marker- assisted breeding and for fine mapping of novel genetic elements controlling leaf size in rice.

Genome-wide selection and introgression of Chinese rice varieties during breeding

China is the largest rice-producing country,but the genomic landscape of rice diversity has not yet been clarified.In this study,we re-sequence 1070 rice varieties collected from China(400)and other regions in Asia(670).Among the six major rice groups(aus,indica-I,indica-II,aromatic,temperate japonica,and tropical japonica),almost all Chinese varieties belong to the indica-II or temperate japonica group.Most Chinese indica varieties belong to indica-II,which consists of two subgroups developed during different phases of rice breeding.The genomic segments underlying the differences between these subgroups span36.32 Mb.The Chinese japonica rice varieties fall into the temperate japonica group,consisting of two subgroups based on their geographical distribution.The genomic segments underlying the differences between these subgroups span 27.69 Mb.These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width.Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups.These findings provide new insights into rice diversity in China that will facilitate the molecular breeding.