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.

Genetic diversity and elite gene introgression reveal the japonica rice breeding in northern China

Abundant genetic diversity and rational population structure of germplasm benefit crop breeding greatly.To investigate genetic variation among geographically diverse set of japonica germplasm,we analyzed 233 japonica rice cultivars collected from Liaoning,Jilin and Heilongjiang provinces of China,which were released from 1970 to 2011 by using 62 simple sequence repeat（SSR） markers and 8 functional gene tags related to yield.A total of 195 alleles（N_a） were detected with an average of 3.61 per locus,indicating a low level of genetic diversity level among all individuals.The genetic diversity of the cultivars from Jilin Province was the highest among the three geographic distribution zones.Moreover,the genetic diversity was increased slightly with the released period of cultivars from 1970 to 2011.The analysis of molecular variance（AMOVA） revealed that genetic differentiation was more diverse within the populations than that among the populations.The neighbor-joining（NJ） tree indicated that cultivar clusters based on geographic distribution represented three independent groups,among which the cluster of cultivars from Heilongjiang is distinctly different to the cluster of cultivars from Liaoning.For the examined functional genes,two or three allelic variations for each were detected,except for IPA1 and GW2,and most of elite genes had been introgressed in modem japonica rice varieties.These results provide a valuable evaluation for genetic backgrounds of current japonica rice and will be used directly for japonica rice breeding in future.

Breeding High-Grain Quality and Blast Resistant Rice Variety Using Combination of Traditional Breeding and Marker-Assisted Selection

We reported a novel rice variety developed by integrating the advantages of high eating quality from Xiangwanxiaa 17(XWX17)and rice blast resistance from Gumei 4(GM4)using a combination of traditional breeding and marker-assisted selection(MAS).Using molecular markers for QTLs/genes responsible for amylose content(AC),fragrance and blast resistance,three inbred lines were selected.

Breeding of Maintainer Line and Sterile Line Brown Planthopper Resistant Rice Using Marker-assisted Selection

Guangxi common wild rice variety brown planthopper highly resistant introgression line HS204 was taken as antigen donor material,hybridization,backcrossing,and molecular marker-assisted selection methods were adopted,to select maintainer line and sterile line materials,so as to provide excellent material foundation for resistance breeding of hybrid rice. Through the marker-assisted selection,it obtained 4 pieces of homozygous resistance gene maintainer line intermediate materials( 100B,101B,102B and 103B),and 2 pieces of resistant sterile line materials( 100A and 103A). All 10 combinations that have testcross with highly resistant sterile 100A showed higher level of brown planthopper resistance: 100A/R2586,100A/KR838,and 100A/KR527 had high resistance level,the others had low to intermediate resistance;100A/KR527,100A/R2586,100A/Minghui 63,100A/Fuhui 838 and 100A/Gui 99 combinations had yield per plant significantly higher than the control group( Teyou 7118),increasing by 14. 45%-49. 26%. The obtained resistant lines are expected to provide a better gene source for the breeding of resistant sterile lines of hybrid rice and the obtained resistant sterile lines can be directly used in the selection of three-line hybrid rice.

Identification of QTLs and Validation of qCd-2 Associated with Grain Cadmium Concentrations in Rice

Cadmium(Cd) is one of heavy metals harmful to human health. As rice is the main staple food in Asia and Cd is easily contaminated in rice, the molecular regulation of Cd accumulation should be explored. In this study, a recombinant inbred population derived from Xiang 743/Katy was grown in Cd-polluted fields and used to map the quantitative trait loci(QTLs) for Cd accumulation in rice grains. We identified seven QTLs distributed on chromosomes 2, 3, 6, 7, 8 and 10. These QTLs displayed phenotypic variances of 58.50% and 40.59% in 2014 and 2015, respectively. Two QTLs, qCd-2 and qCd-7, were identified in both the two years. qCd-2 was detected on the interval of RM250–RM207 on chromosome 2, with an LOD of 2.51 and a phenotypic contribution of 13.75% in 2014, and an LOD of 3.35 and a phenotypic contribution of 14.16% in 2015. qCd-7 co-localized with the cloned qCdT7 on chromosome 7 and may represent the correct candidate. The other five QTLs were detected only in one year. To further confirm the effects of qCd-2, a residual heterozygous line designated as RHL945, with a heterozygous interval of RM263–RM207 on chromosome 2, was selected from the recombinant inbred population and used to develop an F2 population consisting of 155 individual plants. By incorporating further simple sequence repeat markers into the segmental linkage map of the target region, qCd-2 was delimited in the interval of RM5404–RM3774, with an LOD value of 4.38 and a phenotypic contribution of 15.52%. These results reflected the genetic regulation of grain Cd in rice and paved the way for the future cloning of qCd-2.

GNP6,a novel allele of MOC1,regulates panicle and tiller development in rice

The yield of rice is mostly affected by three factors,namely,panicle number,grain number and grain weight.Variation in panicle and grain numbers is mainly caused by tiller and panicle branches generated from axillary meristems(AMs).MOC1 encodes a putative GRAS family nuclear protein that regulates AM formation.Although several alleles of MOC1 have been identified,its variation in germplasm resources remains unclear.In the present study we characterized a novel mocl allele named gnp6 which has a thymine insertion in the coding sequence of the SAW motif in the GRAS domain.This mutation causes arrested branch formation.The SAW motif is necessary for nuclear localization of GNP6/MOC1 where it functions as a transcription factor or co-regulator.Haplotype analysis showed that the coding region of GNP6/MOC1 was conserved without any non-synonymous mutations in 240 rice accessions.However,variation in the promoter region might affect the expression of it and its downstream genes.Joint haplotype analysis of GNP6/MOC1 and MOC3 showed that haplotype combinations H9,H10 and H11,namely MOC1-Hap1 in combination with MOC3-Hap3,MOC3-Hap4 or MOC3-Hap5 could be bred to promote branch formation.These findings will enrich the genetic resources available for rice breeders.

Functional and numerical responses of Cyrtorhinus lividipennis to eggs of Nilaparvata lugens are not affected by genetically modified herbicide-tolerant rice

To safely and sustainably utilize genetic breeding techniques for crop production, greater understanding of the potential effects of genetically modified herbicide-tolerant（GMHT） crops on the ecological functions of predators is required. In the laboratory, we examined the functional and numerical responses of Cyrtorhinus lividipennis Reuter to eggs of brown planthopper（BPH）, Nilaparvata lugens（St？l）, which were reared on GMHT rice Bar68-1; the untransformed parental cultivar, D68; or a BPH-susceptive rice variety, Taichung Native 1. All stages of nymphs and female adult of C. lividipennis, either on GMHT rice or control plants, exhibited typical type II functional responses when fed on BPH eggs; the attacking rate and handling time of C. lividipennis on GMHT rice Bar68-1 was not significantly different from that on D68. The numerical responses of C. lividipennis on GMHT rice or controls fit Beddington＇s model; there were no significant differences in the parameters of numerical responses between GMHT rice Bar68-1 and D68. The results indicated that the functional and numerical responses of C. lividipennis to BPH eggs are not affected by GMHT rice Bar68-1.

Characterization and fine mapping of RTMS10, a semi-dominant reverse thermo-sensitive genic male sterile locus in rice

The discovery and application of environment-sensitive genic male sterile(EGMS) rice germplasm provide an easy method for hybrid rice breeding and have made great contributions to hybrid rice production. Typically, the photoperiod-and thermosensitive GMS(P/TGMS) lines utilized in two-line hybrid systems are male sterile under long day or/and high temperature but fertile under short day or/and low temperature conditions. However, Yannong S(Yn S), a reverse TGMS(rTGMS) line, is sterile under low temperature(<29℃) and fertile under high temperature(>29.5℃). Here, we report a genetic study on the rTGMS trait in Yn S. Interestingly, the F1 plants of the cross between Yn S and a cultivar, L422, were male sterile at 22℃ and completely fertile at 27℃. Moreover, the segregation ratio of fertile and sterile individuals in Yn S/L422 F2 populations changed from 1:3.05 to 2.95:1 when the ambient temperature increased, showing that the rTGMS trait exhibits semidominance in Yn S. We further found a locus on chromosome 10, termed RTMS10, which controls the rTGMS trait in Yn S. We then finely mapped RTMS10 to a ~68 kb interval between markers ID13116 and ID1318 by Yn S/L422 BC6 F2 populations. A near iso-genic line(NIL) NL1 from the BC6 F3 generation was developed and the pollen of NL1 became abnormal from the meiosis stage under low temperature. In summary, we identified an rTGMS locus, RTMS10, and provided co-segregated markers, which could help to accelerate molecular breeding of rTGMS lines and better understand the rTGMS trait in rice.

Marker-Assisted Breeding of Thermo-Sensitive Genic Male Sterile Line 1892S for Disease Resistance and Submergence Tolerance

Rice line 1892S is an elite thermo-sensitive genic male sterile(TGMS)line for two-line hybrid rice production.However,1892S is susceptible to rice blast,bacterial blight and submergence.Here we reported the introduction of blast resistance(R)gene Pi9,bacterial blight R gene Xa21 and submergence tolerance gene Sub1A into 1892S genetic background through backcrossing and marker-assisted selection.The improved TGMS line 31892S and its hybrids conferred disease resistance to rice blast and bacterial blight,and showed submergence tolerance for over 14 d without significant loss of viability.The sterility-fertility conversion of 31892S was similar to that of 1892S.31892S and its derived hybrid rice had similar agronomic traits and grain quality with 1892S and the control hybrid rice,respectively.The newly developed 31892S provided an improved TGMS line for two-line hybrid rice production with disease resistance to rice blast and bacterial blight,and submergence tolerance with no yield penalty or change in grain quality.

OsPEX1,a leucine-rich repeat extensin protein,functions in the regulation of caryopsis development and quality in rice

Rice caryopses are enclosed by outer glumes.The size and dimension of the outer glume are the main determinants of caryopsis size.However,it is unclear whether caryopsis development is completely dependent on the size of the glume,or whether it can grow and expand autonomously despite the constraint of glume enclosure.We report the identification of a mutant line that produces normal-sized glumes with smaller mature caryopses that do not fill the entire glume cavity.The caryopsis phenotype in the pex1 mutant is caused by a reduction in cell size.Os PEX1,a leucine-rich repeat extensin gene,was highly expressed in the developing caryopsis.Overexpression of Os PEX1 driven by a constitutive promoter recapitulated the mutant phenotype,showing that the small-caryopsis phenotype is caused by overexpression of the Os PEX1 gene.Free amino acids,including several essential amino acids,and crude protein were increased in pex1 relative to the wild type,endowing pex1 with improved nutritional quality.Our results suggest that caryopsis development can be genetically uncoupled from maternally controlled glume development and that Os PEX1 might be a new resource for improving nutritional quality of rice cultivars.

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.

Accumulation Characteristics of Protein and Non-Protein Components and Their Correlations with Protein Concentration in Rice Grains

Protein in rice grains is an important source of nutrition for rice consumers.This study mainly aimed to identify the critical factors that determine grain protein concentration in rice.Accumulation parameters,including mean accumulation rate(Rmean)and active accumulation duration(Dactive),for protein and non-protein components and their correlations with protein concentration in rice grains were investigated in field experiments conducted over two years with six rice cultivars.Results showed that grain protein concentration ranged from 9.6%to 11.9%across cultivars and years.Accumulation processes of protein and non-protein components were well fitted by the logistic equation for all six rice cultivars in both years,and the ratio of protein to non-protein for R_(mean) and D_(active) ranged from 0.08 to 0.12 and 1.01 to 1.33,respectively.Grain protein concentration was significantly correlated with protein to non-protein ratio for R_(mean).This study suggests that grain protein concentration is not solely determined by the accumulation of protein or non-protein component,but by the coordination of protein and non-protein accumulation.

Breeding of High Quality Conventional Japonica Type Glutinous Rice Bancangjingnuo

Bangcangjingnuo is a new, mid-maturing conventional Japonica type glutinous rice variety bred by Hunan Rice Research Institute and Hunan Wucai Agricultural Science and Technology Development Co., Ltd. In 2017, the Hunan Crop Variety Examination and Approval Committee approved Bangcangjingnuo. The breeding process of this cultivar was expounded in this study. This cultivar is highly glutinous and waxy, it produces a stable high yield, and it possesses the quality of low temperature resistance. The theoretical yield of Bangcangjingnuo is 8 731.5 kg/hm^2, and the actual output is about 7 422.0 kg/hm^2 according to the 85% discount.Finally, we described the main points of cultivation technique from the perspectives of timely planting and strict seed sterilization.

Genetic Similarity Analysis of Hunan Rice Landraces with Same or Similar Name in Household and Genebank Conservations

This study was conducted to analyze the phenotypic and genotypic similarity or diversity of rice （Oryza sativa L.） landraces in household and hypothermic genebank conservations in Hunan Province and identify the genetic distance between the rice landraces with the same or similar names. A total of 92 accessions of rice landraces were divided into seven groups according to their local names, but the morphological traits showed large variations even within the same group as well as between household and genebank conservations. The SSR marker analysis showed that, in all the groups except Group E, the allelic variations within each subgroup of the household conservation were less than those of the genebank conservation, indicating the household-conserved rice landraces’ many-generation purifcation from natural and artifcial selections in the process of their cultivation year after year; and the similarity coeffcient among the household rice landraces was the highest except for Groups C and E. Thus, the study suggested that the same-name or similar-name rice resources retained by farmers would be valuable for collection and evaluation.

Heat Resistance of Rice Landrace D43 at Anthesis

Rice is extremely sensitive to high temperature, especially at the fowering stage. Identifying new germplasm and breeding heat-resistant rice varieties are therefore essential. After multi-year evaluations, a heat-resistant rice landrace D43 was identifed in our previous research. In this study, the relationship between heat resistance and flower opening time （FOT） was analyzed both in the field and in phytotron. The results showed that high temperature could accelerate fower opening of a range of rice varieties. The D43 showed early morning fowering （EMF） habit in different conditions, and the FOT of which was mainly concentrated in the period of 8：30~10：00 AM under high temperature. The spikelet fertility of D43 was relatively low after exposure to invariably high temperature during fower opening. However, the EMF habit of D43 was conducive to avoiding mid-day high temperature, and therefore increased the spikelet fertility under rising high temperature conditions in the feld and in phytotron. In addition, morphological traits including the anther dehiscence rate, the total number and germinated number of pollens on the stigma were signifcantly correlated with the spikelet fertility, and therefore they could be used to evaluate rice heat resistance at anthesis.

Breeding of a Water-saving Drought-resistant Two-line Hybrid Rice Variety Wanliangyou 1008

Drought is one of the important factors limiting rice production,and the application of new water-saving rice varieties is urgently needed in rice production.Wanliangyou 1008 bred by Institute of Rice Research,Anhui Academy of Agricultural Sciences is a new two line hybrid rice variety with some good traits,including high drought resistance,high yield and good disease resistance.Wanlingyou 1008 was obtained by crossing drought-resistant high-quality restorer line DJ1008 and disease-resistant two-line sterile line Wan 25S.In this paper,the breeding process,characteristics and seed production technology of the variety were described in detail.

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.

Genome-Wide Association Study for Milled Grain Appearance Traits Using Multi-Parent Advanced Generation Intercross Population in Rice

The identification of loci and markers associated with milled grain appearance traits is essential for breeding high-yielding and good-quality rice variety.To detect stable loci for these characteristics,grain length(GL),grain width(GW),grain length/width(GLW),chalkiness degree(CD),chalky-grain rate(CR)and translucency degree(TD)of 378 rice lines were evaluated in three seasons.These lines were derived from a multi-parent advanced generation intercross(MAGIC)population.

Identification of QTLs for seed storability in rice under natural aging conditions using two RILs with the same parent Shennong 265

Seed storability （SS） is an important trait for agronomic production and germplasm preservation in rice （Oryza sativa L.）. Quantitative trait locus （QTL） for seed storability in three storage periods was identified using two sets of recombinant inbred lines （RILs） derived from the crosses with a colnmon female parent Shennong 265 （SN265）. Ten QTLs for seed storability were detected on chromosomes 1, 2, 3, 4, 6, 8, and 12in SL-RILs （SN265/Lijiangxingtuanheigui （LTH））, and a total of 12 QTLs were identified on chromosomes 2, 3, 4, 6, 9, and 10 in SH-RILs （SN265/Luhui 99 （LH99））in different storage periods. Among these QTLs, five major QTLs were identified in more than one storage period. The qSS3-1, qSS3-2, qSS12-1, and qSS12-2 were detected in SL-RILs. Similarly, qSS2-2, qSS2-3, qSS6-2, qSS6-3, qSS6-4, qSS9-1, and qSS9-2 were detected in SH-RILs. In addition, the maximum phenotypic variation was derived from the qSS6-1 and qSS9-2, explaining 53.58 and 29.09%, respectively, while qSS6-1 was a new stable QTL for seed storability. These results provide an opportunity for pyramiding and map-based cloning major QTLs for seed storability in rice.

Discussion on strategy of grain quality improvement for super high yielding japonica rice in Northeast China

japonica rice is mainly distributed in Northeast China and accounts for 44.6% of the total cultivated area of japonica rice in China. The comprehensive using of inter-subspecies heterosis is the main breeding mode of super japonica rice varieties in this region. Improving rice quality at relative high yielding level is the current research focus. Performing crosses between indica and japonica lines allows for the recombination of regulatory genes and genetic backgrounds, leading to complicated genetic rice quality characteristics, which can be used to explore patterns of quality improvement. In the present study, we utilize recombinant inbred lines （RILs） derived from indica-japonica hybridization to analyze the effect factors of rice quality derived from genetic factors, which contain both regulatory genes concerning rice quality and genetic backgrounds＇ random introduction frequency coming from indica （Di value）, and the improvement strategy was further discussed. The regulatory genes involved in amylase content （Wx） and nitrogen utilization efficiency （NRT1.1B） were the major factors affecting the amylose content （AC） and protein content （PC） in RILs, respectively. Both the Di value and the major grain width gene （GS5） had regulatory effects on milled rice width （MRW） in RILs, and their interaction explained the major variance of MRW in the RILs. With the mediation of MRW and chalkiness degree （C）, Di value had a further impact on head rice rate （HR）, which was relatively poor when the Di value was over 40%. In Northeast China, the Di value should be lowered by backcrossing or multiple crosses during the breeding of indica-japonica hybridization to maintain the whole better HR and further to emphasize the use of favorable genes in individual selection.