Genetic bases of source-,sink-,and yield-related traits revealed by genome-wide association study in Xian rice

The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection.

Identification and Analysis of Genetic Diversity Structure Within Pisum Genus Based on Microsatellite Markers

To assesse the genetic diversity among wild and cultivated accessions of 8 taxonomic groups in 2 species, and 5 subspecies under Pisum genus, and to analyze population structure and their genetic relationships among various groups of taxonomy, the study tried to verify the fitness of traditionally botanical taxonomic system under Pisum genus and to provide essential information for the exploration and utilization of wild relatives of pea genetic resources. 197 Pisum accessions from 62 counties of 5 continents were employed for SSR analysis using 21 polymorphic primer pairs in this study. Except for cultivated field pea Pisum sativum ssp. sativum var. sativum （94 genotypes）, also included were wild relative genotypes that were classified as belonging to P. fulvum, P. sativum ssp.abyssinicum, P. sativum ssp. asiaticum, P. sativum ssp. transcaucasicum, P. sativum ssp. elatius var. elatius, P. sativum ssp. elatius var. pumilio and P. sativum ssp. sativum var. arvense （103 genotypes）. The PCA analyses and 3-dimension PCA graphs were conducted and drawn by NTSYSpc 2.2d statistical package. Nei78 genetic distances among groups of genetic resources were calculated, and cluster analysis using UPGMA method was carried out by using Popgene V1.32 statistical package, the dendrogram was drawn by MEGA3.1 statistical package. Allelic statistics were carried out by Popgene V1.32. The significance test between groups of genotypes was carried out by Fstat V2.9.3.2 statistical package. 104 polymorphic bands were amplified using 21 SSR primer pairs with unambiguous unique polymorphic bands. 4.95 alleles were detected by each SSR primer pair in average, of which 65.56% were effective alleles for diversity. PSAD270, PSAC58, PSAA18, PSAC75, PSAA175 and PSAB72 were the most effective SSR pairs. SSR alleles were uniformly distributed among botanical taxon units under Pisum genus, but significant difference appeared in most pairwise comparisons for genetic diversity between taxon unit based groups of genetic resources. Genetic diversity level of wild species P. fulvum was much lower than the cultivated species P. sativum. Under species P. sativum, P. sativum ssp. sativum var. sativum and P. sativum ssp. asiaticum were the highest in gentic diversity, followed by P. sativum ssp. elatius var. elatius and P. sativum ssp. transcaucasicum, P. sativum ssp. elatius var. pumilio, P. sativum ssp. sativum vat. arvense and P. sativum ssp. abyssinicum were the lowest. Four gene pool clusters were detected under Pisum genus by using PCA analysis. Gene pool ＂fulvum＂ mainly consisted of wild species Pisum fulvum, gene pool ＂abyssinicum＂ mainly consisted of P. sativum ssp. abyssinicum, and gene pool ＂arvense＂ mainly consisted of P. sativum ssp. sativum var. arvense. While gene pool ＂sativum＂ were composed by 5 botanical taxon units, they are P. sativum ssp. asiaticum, P. sativum ssp. elatius var. elatius, P. sativum ssp. transcaucasicum, P. sativum ssp. elatius var. pumilio and P. sativum ssp. sativum var. sativum. ＂sativum＂ gene pool constructed the primary gene pool of cultivated genetic resources; ＂fulvum＂ gene pool, ＂abyssinicum＂ gene pool and ＂arvense＂ gene pool together constructed the secondary gene pool of cultivated genetic resources. Pairwise Nei78 genetic distance among botanical taxon based groups of pea genetic resources ranged from 7.531 to 35.956, 3 large cluster groups were identified based on the UPGMA dendrogram. Group Ⅰ equals to ＂sativum＂ and ＂arvense＂ gene pools, Group Ⅱ equals to ＂abyssinicum＂ gene pool, and Group Ⅲ equals to ＂fulvum＂ gene pool. The UPGMA clustering results generally supporting the PCA clusting results. There were significant differences among most botanical groups under Pisum genus, with clear separation of four gene pools for genetic diversity structure. The research results partially support the traditional botanical taxonomy under Pisum genus, and pointed out its advantage and shortcoming. In order to broaden the genetic bases of pea varieties, the genetic potentials in the four gene pools should be thoroughly exploited.

Genetic background effects on QTL and QTL × environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice

QTLs for quantitative traits are influenced by genetic background(GB) and environment.Identification of QTL with GB independency and environmental stability is prerequisite for effective marker-assisted selection(MAS). In this study, QTLs and QTL × environment interactions affecting grain yield per plant(GY) and its component traits, filled grain number per panicle(FGN), panicle number per plant(PN) and 1000-grain weight(TGW) across six environments were dissected using two sets of reciprocal introgression lines(ILs) derived from the cross Lemont × Teqing and SNP genotypic data. ANOVA indicated that the differences among genotypes and environments within each set of ILs were highly significant for all traits. A total of 72 distinct QTLs for GY and its component traits including 15 for GY, 25 for FGN, 18 for PN, and 29 for TGW were detected over the six environments. Most QTLs(87.4%) showed significant QTL × environment interactions(QEIs) and appeared to be more or less environment-specific. Among 72 QTLs, 15(20.8%) QTLs and 12(16.7%) QEIs were commonly identified in both backgrounds, indicating QTL especially QEI for yield and its component traits had strong GB effects. Four QTL regions affecting GY and its component traits, including S1269707–S4288071, S16661497–S17511092, and S35861863–S36341768 on chromosome 3, and S4134205–S7643153 on chromosome 5, were detected in both backgrounds and coincided with cloned genes for yield-related traits. These regions can be the targeted in rice breeding for high yield potential through MAS. Application of QTL main effects and their environmental interaction effects in MAS was discussed in detail.

Dominant early heading without yield drag in a sister-line BC breeding progeny DEH_229 is controlled by multiple genetic factors with maineffect loci

Dominant early heading(DEH)in rice(Oryza sativa L.)is of interest in both breeding and genetics.The genetic mechanisms underlying DEH have remained largely unclear.We have developed a near-isogenic DEH line without yield drag named DEH_229 by sister-line backcross(BC)breeding with MH63,a restorer,as the genetic background.We conducted a pilot genetic investigation under both short-day(SD)and long-day(LD)conditions.The DEH line harbored only 1.06%variation in the genome sequence relative to MH63.The variants were distributed throughout the genome.Using QTL mapping by sequencing(QTL-seq)on an F_(2) population derived from a cross of MH63×DEH_229,57 loci were detected under the SD condition.Joint mapping employing a genome-wide association study with accessions from the 3000 rice genome sequencing project(3K-RG),reduced the number of QTL by 43.9%.Using Rice Functional Genomics&Breeding(RFGB)database,the number of SNP cluster regions within the QTL regions reduced by 27.3%.Further comparison of the genome variation between DEH_229 and MH63 in addition to gene annotation information revealed a new DEH allele of DTH3 with multiple variable sites as a possible major factor underlying the early-heading phenotype of DEH_229.An InDel marker,ZMEH_1,was designed based on the variation between DEH_229 and MH63 within this region.It accounted for 86.0%of heading date variation under both SD and LD conditions in 109 randomly chosen progeny derived from extreme lines of the MH63×DEH_229 population.This study reveals the genetic complexity of DEH in the near-isogenic line and may provide useful material and marker information for plant molecular breeding.

Improving Drought Tolerance of Rice by Designed QTL Pyramiding

Drought is the most important factor limiting rice yields in the rainfed areas of Asia. To overcome the problem, we developed a new strategy 'designed QTL pyramiding' to more effi ciently develop drought tolerant (DT)

Molecular mechanisms of salinity tolerance in rice

Salinity is one of the major abiotic stresses which impose constraints to plant growth and production.Rice(Oryza sativa L.)is one of the most important staple food crops and a model monocot plant.Its production is expanding into regions that are affected by soil salinity,requiring cultivars more tolerant to saline conditions.Understanding the molecular mechanisms of such tolerance could lay a foundation for varietal improvement of salt tolerance in rice.In spite of extensive studies exploring the mechanism of salt tolerance,there has been limited progress in breeding for increased salinity tolerance.In this review,we summarize the information about the major molecular mechanisms underlying salinity tolerance in rice and further discuss the limitations in breeding for salinity tolerance.We show that numerous gene families and interaction networks are involved in the regulation of rice responses to salinity,prompting a need for a comprehensive functional analysis.We also show that most studies are based on whole-plant level analyses with only a few reports focused on tissue-and/or cell-specific gene expression.More details of salt-responsive channel and transporter activities at tissue-and cell-specific level still need to be documented before these traits can be incorporated into elite rice germplasm.Thus,future studies should focus on diversity of available genetic resources and,particular,wild rice relatives,to reincorporate salinity tolerance traits lost during domestication.

Dissection of heterosis for yield and related traits using populations derived from introgression lines in rice

Despite the great success achieved by the exploitation of heterosis in rice,the genetic basis of heterosis is still not well understood.We adopted an advanced-backcross breeding strategy to dissect the genetic basis of heterosis for yield and eight related traits.Four testcross(TC) populations with 228 testcross F1 combinations were developed by crossing57 introgression lines with four types of widely used male sterile lines using a North Carolina II mating design.Analysis of variance indicated that the effects of testcross F1 combinations and their parents were significant or highly significant for most of the traits in both years,and all interaction effects with year were significant for most of the traits.Positive midparent heterosis(HMP) was observed for most traits in the four TC populations in the two years.The relative HMPlevels for most traits varied from highly negative to highly positive.Sixty-two dominant-effect QTL were identified for HMPof the nine traits in the four TC populations in the two years.Of these,22 QTL were also identified for the performance of testcross F1.Most dominant-effect QTL could individually explain more than 10% of the phenotypic variation.Four QTL clusters were observed including the region surrounding the RM9–RM297 region on chromosome 1,the RM110–RM279–RM8–RM5699–RM452 region on chromosome 2,the RM5463 locus on chromosome 6 and the RM1146–RM147 region on chromosome 10.The identified QTL for heterosis provide valuable information for dissecting the genetic basis of heterosis.

Detection of Drought-Related Loci in Rice at Reproductive Stage Using Selected Introgressed Lines

The present study was carried out to illustrate high-efficient detection of quantitative trait loci （QTLs） with selected introgression lines （ILs） and the existence of ＇hidden genes＇ conferring drought tolerance （DT）. 52 selected DT ILs, derived from BC2Fz population developed by crossing and backcrossing the susceptible recurrent parent （RP） IR64 with the susceptible donor Khazar were planted under irrigation and drought condition. Four important agronomic traits, e.g., grain yield （GY）, heading date （HD）, panicle numbers per plant （PN）, and plant height （PH） were evaluated and 83 SSR polymorphic molecular markers were used for genotypic analysis. Chi-square test based on genetic hitch-hiking and one-way analysis of variances （ANOVA） were used to detect drought-related loci. Nine and 36 loci were detected by chi-square test and one-way ANOVA, respectively. Five common loci were observed by comparing the results of the two methods, among which two QTLs linked with RM7, and RM241 were detected under irrigation condition, both of the favorable alleles were from RP and explained 13% phenotypic variation （PV） for GY and 28% PV for PH, respectively. The other three QTLs linked with RM 163, RM 18, and RM270 were detected under drought condition, the favorable alleles were all from the donor and explained 10, 24, and 19% PV for HD, PH, and PH, respectively. Five common loci were observed by comparing the results of chi-square test and one-way ANOVA including two QTLs （one for GY and one for PH） under irrigation condition and three QTLs （one for HD and two for PH） under drought condition. By combining phenotypic and genotypic analysis, drought escape could be inferred as the main mechanism for drought tolerance in the present study. The results in present study suggested that the selected ILs population analyzed by chi-square test and one-way ANOVA was quite effective for DT QTL detection with low inputs and could also produce useful materials for breeding with wide genetic diversity for drought tolerance.

Flower Development and Photoperiodic Control of Flowering in Rice

Floral transition,which is referred to as a plant＇s transition from vegetative stage to reproductive stage,is considered to be a critical developmental switch in higher plants,for a timely flowering is a major factor of reproductive success.Endogenous and environmental cues,such as photoperiod,light quality,plant hormones concentrations and temperature,provide information to the plants whether the environment is favorable for flowering.These cues promote,or prevent,flowering through a complex genetic network,mediated by a careful orchestration of temporal and spatial gene expression.One of such cues is photoperiod.Rice（Oryza sativa L.） serves as a powerful model species for the understanding of flowering in higher plants,including flower development and photoperiodic control of flowering.In this review,we overviewed and discussed the flower development and its model.We also overviewed the photoperiodic pathways in rice flowering control,and summarized the pathways at molecular level.

Proteomics Identification of Differentially Expressed Leaf Proteins in Response to Setosphaeria turcica Infection in Resistant Maize

Northern corn leaf blight （NCLB）, caused by the heterothallic ascomycete fungus Setosphaeria turcica, is a destructive foliar disease of maize and represents a serious threat to maize production worldwide. A comparative proteomic study was conducted to explore the molecular mechanisms underlying the defense responses of the maize resistant line A619 Ht2 to S. turcica race 13. Leaf proteins were extracted from mock and S. turcica-infected leaves after inoculated for 72 h and analyzed for differentially expressed proteins using two-dimensional electrophoresis and mass spectrometry identification. 137 proteins showed reproducible differences in abundance by more than 2-fold at least, including 50 up-regulated proteins and 87 down-regulated proteins. 48 protein spots were successfully identified by MS analysis, which included 10 unique, 6 up-regulated, 20 down-regulated and 12 disappeared protein spots. These identified proteins were classified into 9 functional groups and involved in multiple functions, particularly in energy metabolism （46%）, protein destination and storage （12%）, and disease defense （18%）. Some defense-related proteins were upregulated such as 13-glucosidase, SOD, polyamines oxidase, HSC 70 and PPIases; while the expressions of photosynthesis- and metabolism-related proteins were down-regulated, by inoculation with S. turcica. The results indicated that a complex regulatory network was functioned in interaction between the resistant line A619 Ht2 and S. turcica. The resistance processes of A619 Ht2 mainly resided on directly releasing defense proteins, modulation of primary metabolism, affecting photosyntesis and carbohydrate metabolism.

QTL underlying iron and zinc toxicity tolerances at seedling stage revealed by two sets of reciprocal introgression populations of rice(Oryza sativa L.)

Iron and zinc are two trace elements that are essential for rice. But they are toxic at higher concentrations, leading to severe rice yield losses especially in acid soils and inland valleys. In this study, two reciprocal introgression line(IL) populations sharing the same parents were used with high-density SNP bin markers to identify QTL tolerant to iron and zinc toxicities. The results indicated that the japonica variety 02,428 had stronger tolerance to iron and zinc toxicities than the indica variety Minghui 63. Nine and ten QTL contributing to iron and zinc toxicity tolerances,respectively, were identified in the two IL populations. The favorable alleles of most QTL came from 02,428. Among them, q FRRDW2, q ZRRDW3, and q FRSDW11 appeared to be independent of genetic background. The region C11S49–C11S60 on chromosome 11 harbored QTL affecting multiple iron and zinc toxicity tolerance-related traits, indicating partial genetic overlap between the two toxicity tolerances. Our results provide essential information and materials for developing excellent rice cultivars with iron and/or zinc tolerance by marker-assisted selection(MAS).

Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high-throughput RNA sequencing

Plant microRNAs(miRNAs)play important roles in biological processes such as development and stress responses.Although the diverse functions of miRNAs in model organisms have been well studied,their function in wild rice is poorly understood.In this study,high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata.A total of 603 miRNAs,380 known rice miRNAs,72 conserved plant miRNAs,and151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes.Additionally,99 and 79 miRNAs were expressed exclusively or differentially,respectively,in the two tissues,and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes.Functional annotation of these targets suggested that transcription factors,including squamosa promoter binding proteins and auxin response factors,function in rhizome growth and development.The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR,and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets.Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′end amplification.These results provide valuable information on the composition,expression and function of miRNAs in O.longistaminata,and will aid in understanding the molecular mechanisms of rhizome development.

The Power of Inbreeding： NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice （Oryza sativa L.）, which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5~ and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SN Ps in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice,japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.

“种质资源组学”数据共享与挖掘通用模式:以SoyFGB v2.0为例

Soybean(Glycine max(L.)Merr.)is a crop that originated in China.Soybean is one of the most important sources of edible vegetable protein and oil,and it has become a model legume species in genomic research.Worldwide gene banks,such as the National Crop Genebank of China(NCGC)and the United States Department of Agriculture-Agricultural Research Service(USDA-ARS)Soybean Germplasm Collection.

Genome and Comparative Transcriptomics of African Wild Rice Oryza Iongistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility

Dear Editor, Oryza Iongistaminata is an African wild rice species with AA genome type possessing special traits that are highly valued for improving cultivated rice, such as strong resistance to biotic and abiotic stresses （Song et al., 1995） for improving resistance of cultivars, rhizomatousness for perennial breeding （Glover et al., 2010）, and self-incompatibility （SI） for new ways to produce hybrid seeds （Ghesquiere, 1986）. Deciphering the genome of O. Iongistaminata will be the key to uncovering the mechanism of these hallmark traits and improving cultivated rice.