Fine mapping and characterization of a major QTL for grain length,QGl.cau-2D.1,that has pleiotropic effects in synthetic allohexaploid wheat

Grain size is one of the determinants of grain yield,and identifying the genetic loci that control grain size will be helpful for increasing grain yield.In our previous study,a quantitative trait locus(QTL)for grain length(GL),QGl.cau-2D.1,was identified from an F2 population developed from the cross between the natural(TAA10)and synthetic(XX329)allohexaploid wheat.In the present study,we mainly fine mapped and validated its genetic effects.To this end,multiple near-isogenic lines(NILs)were obtained through marker-assisted selection with TAA10 as the recurrent parent.The secondary populations derived from 25 heterozygous recombinants were used for fine mapping of QGl.cau-2D.1,and the allele from XX329 significantly increased GL,thousand-grain weight(TGW),total spikelet number per spike(TSN)and spike compactness(SC).Using NILs for XX329(2D+)and TAA10(2D−),we determined the genetic and pleiotropic effects of QGl.cau-2D.1.The target sequences were aligned with the wheat reference genome RefSeq v2.1 and spanned an~0.9 Mb genomic region.TraesCS2D03G0114900(ortholog of Os03g0594700)was predicted as the candidate gene based on whole-genome re-sequencing and expression analyses.In summary,the map-based cloning of QGl.cau-2D.1 will be useful for improving grain weight with enhanced GL and TSN.

Fine mapping and candidate gene analysis of qGL10 affecting rice grain length

Grain size influences the yield and quality of rice(Oryza sativa L.),and grain length is one of the component traits of grain size.In this study,a near-isogenic line LB3 with long grain size was constructed using japonica rice cultivar 02428,with short grain size,as the recipient parent and indica rice cultivar ZYX,with long grain size,as the donor parent,by multi-generation backcrossing and selfing.BSA-seq was used for preliminary QTL mapping and InDel markers were developed to fine map the locus.The major QTL,tentatively named qGL10,for grain length was located in a 128.45 kb region of chromosome 10.Combined with haplotype analysis of rice varieties,expression pattern analysis of candidate genes suggested LOC_Os10g39130(OsMADS56)as a candidate gene.Sequence alignment of OsMADS56 in 02428 and LB3 revealed that there were 15 SNPs in the promoter region and four in the coding region.Further haplotype analysis suggested that SNP9(G/A)located in the TGTCACA motif might account for the different expression levels of OsMADS56 in 02428 and LB3.These results lay a foundation for the application of qGL10 in molecular breeding of new rice varieties.

Poaceae Orthologs of Rice OsSGL,DUF1645 Domain-Containing Genes,Positively Regulate Drought Tolerance,Grain Length and Weight in Rice

Grain yield is a polygenic trait that can be influenced by environmental factors and genetic compositions at all plant growth stages.Currently,the molecular mechanisms behind the coordination of the interaction between grain yield-related traits remain unknown.In this study,we characterized the function of four STRESS_tolerance and GRAIN_LENGTH(Os SGL)Poaceae ortholog genes that are transcribed into DUF1645 domain-containing proteins in relation to the grain length,grain weight,and drought stress-tolerance of rice.The transgenic plants with overexpressing or heterologous high levels of Poaceae OsSGL ortholog genes exhibited longer grain size than the wild type plants.Larger cells were seen in panicles of the four transgenic lines with paraffin sectioning and scanning electron microscopy analyses.In addition,four Poaceae OsSGL ortholog genes positively affected the drought tolerance of rice.Four transgenic plants displayed higher resistance to drought stress at the seedling and vegetative stages.RNA-sequencing and qRT-PCR results indicated that over-or heterologous-expression of four Poaceae OsSGL ortholog genes also affected the transcriptome of rice plants.These genes may play a role in auxin and cytokinin biosynthesis and their transduction pathways.Taken together,these results suggested that the four OsSGL orthologs have a conserved function in the regulation of stress-tolerance and cell growth by modulating hormonal biosynthesis and signaling.

QTL-Seq Identified a Major QTL for Grain Length and Weight in Rice Using Near Isogenic F_2 Population

Mapping and isolation of quantitative trait loci(QTLs)or genes controlling grain size or weight is very important to uncover the molecular mechanisms of seed development and crop breeding.To identify the QTLs controlling grain size and weight,we developed a near isogenic line F_2(NIL-F_2)population,which was derived from a residual heterozygous plant in an F_7 generation of recombinant inbred line(RIL).With the completion of more than 30×whole genome re-sequencing of the parents,two DNA bulks for large and small grains,a total of 58.94 Gb clean nucleotide data were generated.A total of455 262 single nucleotide polymorphisms(SNPs)between the parents were identified to perform bulked QTL-seq.A candidate genomic region containing SNPs strongly associated with grain length and weight was identified from 15 to 20 Mb on chromosome 5.We designated the major QTL in the candidate region as q TGW5.3.Then,q TGW5.3 was further validated with PCR-based conventional QTL mapping method through developing simple sequence repeat and Insertion/Deletion markers in the F_2 population.Furthermore,recombinants and the progeny tests delimited the candidate region of q TGW5.3 to 1.13 Mb,flanked by HX5009(15.15 Mb)and HX5003(16.28 Mb).A set of NILs,selected from the F_2 population,was developed to evaluate the genetic effect of q TGW5.3.Significant QTL effects were detected on grain length,grain width and 1000-grain weight of H12-29 allele with 1.14 mm,-0.11 mm and 3.11 g,which explained 99.64%,95.51%and 97.32%of the phenotypic variations,respectively.

OsDA1 positively regulates grain width in rice

The size and shape of rice grains influence their yield and commercial value.We investigated the role of OsDA1,a rice homolog of the Arabidopsis DA1 gene,in regulating grain size and shape.OsDA1 was highly expressed in young spikelets and glumes.Its overexpression led to enlarged seeds with increased width and decreased length/width ratio(LWR)and knocking out OsDA1 reduced grain width and increased grain length and LWR.A R310K point mutation in the DA1-like domain is a potential target for breeding for increased grain width and length.OsDA1 interacted with TCP gene-family proteins to regulate grain size and shape.Our findings deepen our understanding of the molecular mechanisms underlying grain size regulation and provide useful information for improving grain yield.

Mapping of qGL7-2, a grain length QTL on chromosome 7 of rice

A residual heterozygous line （RHL） carrying a heterozygous segment between two S SR loci RM 11 and RM134 on the rice chromo- some 7 was selected from a set of recombinant inbred lines from the cross D50 （javanica）/HB277 （indica）. The former parent produces much longer grains than the latter. Selfed progenies of this selection were analyzed genotypically （SSRs） and phenotypically （grain length）. Grain length was discontinuously variable in the mapping populations, allowing for the placement of this QTL qGL7-2 within a -4.8 cM interval defined by RM351 and RM234. A set of new markers within this region were developed, which narrowed the QTL to a 278 kb region defined by the markers Indell and RM21945. This region contains 49 predicted genes. The results also suggest that the novel allele for grain length will be used for the application of marker assisted selection for the improvement of grain length.

A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice

Grain size is one of the most important factors that control rice yield,as it is associated with grain weight(GW).To date,dozens of rice genes that regulate grain size have been isolated;however,the regulatory mechanism underlying GW control is not fully understood.Here,the quantitative trait locus qGL5 for grain length(GL)and GW was identified in recombinant inbred lines of 9311 and Nipponbare(NPB)and fine mapped to a candidate gene,OsAUX3.Sequence variations between 9311 and NPB in the OsAUX3 promoter and loss of function of OsAUX3 led to higher GL and GW.RNA sequencing,gene expression quantification,dual-luciferase reporter assays,chromatin immunoprecipitation-quantitative PCR,and yeast one-hybrid assays demonstrated that OsARF6 is an upstream transcription factor regulating the expression of OsAUX3.OsARF6 binds directly to the auxin response elements of the OsAUX3 promoter,covering a single-nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung,and thereby controls GL by altering longitudinal expansion and auxin distribution/content in glume cells.Furthermore,we showed that miR167a positively regulate GL and GW by directing OsARF6 mRNA silencing.Taken together,our study reveals that a novel miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice,providing a potential target for the improvement of rice yield.

Natural variations in grain length 10(GL10)regulate rice grain size

Grain size is an important determinant of grain weight and yield in rice.Although several genes related to grain size have been identified,natural variations in these genes that affect grain size are poorly characterized.Here,we describe the grain length QTL GL10,encoding MADS56,which positively regulates grain length and grain weight.A natural allelic variation of NIL-gl10,containing an~1.0-kb deletion in the first exon that abolishes its transcription,results in shorter grain length,lower grain weight and delayed flowering in gl10 plants.The knockout of GL10 in the HJX74 background leads to grain phenotypes similar to that of NIL-gl10,while overexpression of GL10 results in increased grain length and weight and earlier heading date.GL10 regulates grain length by promoting greater longitudinal cell growth in the grain glume.Additionally,GL10 participates in the regulation of gibberellic acid(GA)signaling pathway genes in young panicle tissues.Analysis of GL10 haplotypes shows obvious divergence between the japonica and indica lineages.Our findings reveal an allelic variation of GL10 that may explain differences in grain length among modern cultivars and could be used to breed rice varieties with optimized grain shape.

Identification and validation of major QTL for grain size and weight in bread wheat(Triticum aestivum L.)

Grain size and weight are key components of wheat yield.Exploitation of major underlying quantitative trait loci(QTL)can improve yield potential in wheat breeding.A recombinant inbred line(RIL)population was constructed to detect QTL for thousand-grain weight(TGW),grain length(GL)and grain width(GW)across eight environments.Genomic regions associated with grain size and grain weight were identified on chromosomes 4A and 6A using bulked segregant exome sequencing(BSE-Seq)analysis.After constructing genetic maps,six major QTL detected in at least four individual environments and in best linear unbiased estimator(BLUE)datasets,explained 7.50%-23.45%of the phenotypic variation.Except for QGl.cib-4A,the other five QTL were co-located in two regions,namely QTgw/Gw.cib-4A and QTgw/Gw/Gl.cib-6A.Interactions of these QTL were analyzed.Unlike QTgw/Gw/Gl.cib-6A,QTgw/Gw.cib-4A and QGl.cib-4A had no effect on grain number per spike(GNS).The QTL were validated in a second cross using Kompetitive Allele Specific PCR(KASP)markers.Since QTgw/Gw.cib-4A was probably a novel locus,it and the KASP markers reported here can be used in wheat breeding.TraesCS4A03G0191200 was predicted to be potential candidate gene for QTgw/Gw.cib-4A based on the sequence differences,spatiotemporal expression patterns,gene annotation and haplotype analysis.Our findings will be useful for fine mapping and for marker-assisted selection in wheat grain yield improvement.

基于55K芯片小麦籽粒相关性状的QTL定位分析

为了进一步挖掘小麦籽粒相关性状的主效QTL位点,探索籽粒性状之间的遗传关系,利用籽粒性状差异较大的小麦品种安农859和武农988构建的124份DH群体为研究材料,分别测定2 a 7个环境下的粒长、粒宽及千粒质量表型值,开展籽粒性状多元回归分析,并基于DH群体的55K芯片数据进行籽粒相关性状QTL检测。结果表明,多元回归分析中,粒宽对千粒质量的贡献最大。通过完备区间作图对籽粒性状进行QTL定位,除6D和7B染色体外,其他19条染色体上共检测到69个有关籽粒性状的QTL,包括24个千粒质量QTL、28个粒长QTL、17个粒宽QTL,单个QTL的表型解释率为6.87%~27.74%。其中,7A染色体上粒长相关的Qgl.ahau-7A.1在7个环境及BLUP下均被检测到,表型解释率为9.48%~22.26%,加性效应为0.11~0.21 mm,物理区间4.91 Mb(AX-110430243~AX-110442528),可能为新的主效QTL。因此,Qgl.ahau-7A.1位点可作为后续精细定位和分子标记辅助育种重点关注的区域。

小麦E3泛素连接酶基因TaSINA-3A与多种环境下的株高和千粒重相关

E3泛素连接酶SINA(seven in absentia)家族参与植物的生长发育、免疫共生并响应逆境胁迫。本研究克隆了位于小麦染色体3A上的TaSINA-3A基因,其基因组序列长度为3897 bp,其中启动子区为2001 bp,基因序列为1896 bp,编码244个氨基酸,在50~91位氨基酸处有一个RING(really interesting new gene)保守结构域。RT-qPCR结果显示,TaSINA-3A基因在小麦的各个发育阶段的不同组织中均有表达。序列多态性分析表明,在TaSINA-3A的启动子区存在33个SNP(single nucleotide polymorphism)位点,编码区有4个SNP位点。基于启动子区的变异位点SNP-159、SNP-418和SNP-1286开发分子标记,扫描小麦自然群体,并与表型性状进行关联分析。结果表明,标记CAPS-159与多种环境下的株高和倒二节长显著相关,SNP-159-C是倒二节较短的矮秆等位变异,标记dCAPS-418分别与多种环境下的穗长和千粒重显著关联,SNP-418-A是长穗、高千粒重的优异等位变异;TaSINA-3A负调控穗和籽粒的发育,TaSINA-3A的表达可能受到MYC转录因子的抑制;在我国小麦育种进程中SNP-418-A受到正向选择,在育成品种中的频率逐步增加,但尚未充分利用。研究结果为深入探讨小麦株高、倒二节长及产量的形成机制提供参考,并为培育高产稳产广适新品种提供了基因资源。

A gain-of-function mutation of OsMAPK6 leads to long grain in rice

Grain size is one of the most important agronomic traits controlling grain yield. Development of novel germplasm with large grains would be beneficial for crop improvement. We report the genetic identification and functional analysis of the LONG GRAIN 6(LOG6) gene, which is identical to MITOGENACTIVATED PROTEIN KINASE 6(OsMAPK6), affecting grain length of rice. Map-based cloning revealed that the long-grain phenotype of log6-D results from a glutamine(E) to lysine(K) mutation in the conserved TEY motif of OsMAPK6. In near-isogenic lines(NILs), the log6-D allele increased grain length and grain yield of Guichao 2(GC2), Teqing(TQ), and 93–11. Sequence analysis revealed 10 OsMAPK6 haplotypes,with xian(indica) and geng(japonica) harboring different haplotypes. Our findings shed light on the function of MAPKs and offer a novel dominant allele for improving the grain yield of rice.

粳稻种质资源粒长全基因组关联分析及候选基因筛选

为挖掘与水稻粒长相关的候选基因,以139份西北早粳稻核心种质资源为材料,结合重测序获得的255501个高质量SNPs,利用FarmCPU模型对水稻粒长进行全基因组关联分析,将显著SNPs上下游各延伸50 kb作为候选区间,再将候选区间内CDS区存在差异的基因进行功能注释和单倍型分析。结果表明,139份水稻种质粒长变异系数为9.18%,且近似正态分布,在阈值-log_(10)(p)≥6.41条件下,FarmCPU模型分别在3号、5号、7号、10号染色体上检测到7个显著且有代表性的SNPs,在候选区间内筛选出2个水稻粒长的候选基因。LOC_Os05g10420和LOC_Os05g10560都编码表达蛋白,LOC_Os05g10420通过分型共分为2个单倍型,且含有Hap1的种质粒长极显著低于含有Hap2的种质粒长;LOC_Os05g10560通过分型共分为3个单倍型,含有Hap1的种质粒长极显著低于含有Hap2和Hap3的种质粒长。

Creation of Long-grain Fragrant Japonica Rice by Genome Editing

To create the japonica germplasm with long grain and fragrance,we edited GS3 and OsBADH2 of a japonica rice cultivar Chunjiang 151 by using CRISPR/Cas9 system for multiplex genome editing.10 long-grain fragrant japonica rice plants without transgenic components were obtained.Compared with those of Chunjiang 151,the grain length,thousand-grain weight,and yield per plant of the edited line increased 12.20%,18.45%,and 8.31%,respectively.We created the fragrant japonica rice line with improved grain length and yield,which enriched the germplasm resource of japonica rice and provided reference for the improvement of rice quality.

Fine-Mapping of qTGW1.2a, a Quantitative Trait Locus for 1000-Grain Weight in Rice

Thousand-grain weight (TGW) is a key component of grain yield in rice. This study was conducted to validate and fine-map qTGW1.2a, a quantitative trait locus for grain weight and grain size previously located in a 933.6-kb region on the long arm of rice chromosome 1. Firstly, three residual heterozygotes (RHs) were selected from a BC2F11 population of the indica rice cross Zhenshan 97 (ZS97)///ZS97//ZS97/Milyang 46. The heterozygous segments in these RHs were arranged successively in physical positions, forming one set of sequential residual heterozygotes (SeqRHs). In each of the populations derived, non-recombinant homozygotes were identified to produce near isogenic lines (NILs) comprising the two homozygous genotypes. The NILs were tested for grain weight, grain length and grain width. QTL analyses for the three traits were performed. Then, the updated QTL location was followed for a new run of SeqRHs identification-NIL development-QTL mapping. Altogether, 11 NIL populations derived from four sets of SeqRHs were developed and used. qTGW1.2a was finally delimitated into a 77.5-kb region containing 13 annotated genes. In the six populations segregating this QTL, which were in four generations and were tested across four years, the allelic direction of qTGW1.2a remained consistent and the genetic effects were stable. For TGW, the additive effects ranged from 0.23 to 0.38 g and the proportions of phenotypic variance explained ranged from 26.15% to 41.65%. These results provide a good foundation for the cloning and functional analysis of qTGW1.2a.

Fine mapping of qTGW10-20.8, a QTL having important contribution to grain weight variation in rice

Grain weight is one of themost important determinants of grain yield in rice.In this study,QTL analysis for grain weight,grain length,and grainwidthwas performed using populations derived from crosses between major parental lines of three-line indica hybrid rice.A total of 27 QTL for grain weight were detected using three recombinant inbred line populations derived from the crosses Teqing/IRBB lines,Zhenshan 97/Milyang 46,and Xieqingzao/Milyang 46.Of these,10 were found in only a single population and the other 17 in two or all three populations.Nine of the 17 common QTL were located in regions where no QTL associated with grain weight have been cloned and onewas selected for fine-mapping.Eight populations segregating in an isogenic background were derived from one F7 residual heterozygote of Teqing/IRBB52.The target QTL,qTGW10-20.8 controlling grain weight,grain length,and grain width,was localized to a 70.7-kb region flanked by InDel markers Te20811 and Te20882 on the long arm of chromosome 10.The QTL region contains seven annotated genes,ofwhich six encode proteins with known functional domains and one encodes a hypothetical protein.One of the genes,Os10g0536100 encoding the MIKC-type MADS-box protein OsMADS56,is the most likely candidate for qTGW10-20.8.These results provide a basis for cloning qTGW10-20.8,which has an important contribution to grain weight variation in rice.

Effects of Interface and Grain Boundary on the Electrical Resistivity of Cu/Ta Multilayers

The electrical resistivity of Cu/Ta multilayers deposited by radio-frequency magnetron sputtering on a polyimide substrate was investigated as a function of monolayer thickness. It is found that the resistivity of the multilayer increases with decreasing monolayer thickness from 500 nm to 10 nm. Two significant effects of layer interface scattering and grain boundary scattering were identified to dominate electronic transportation behavior in the Cu/Ta multilayers at different length scales. The electrical resistivity of the multilayer with monolayer thickness ranging from nanometer to submicron scales can be well described by a newly-proposed Fuchs-Sandheimair （F-S） and Mayadas-Shatzkes （M-S） combined model.

Root Length Density in Maize/Cowpea Intercropping under a Basin Tillage System in a Semi-Arid Area of Zimbabwe

A study to assess the effect of intercropping maize (Zea mays L.) and cowpea (Vigna unguiculata L.) within the same basin or outside the basin on root length density (RLD) was conducted at the International Crop Research Institute for Semi-Arid Tropics (ICRISAT) Matopos Research Station from December 2009 to April 2010. The experiment was laid out in a Randomised Complete Block Design (RCBD) with four treatments replicated four times namely;sole maize, sole cowpea, maize-cowpea intercrop with cowpea and maize planted within the same basin and maize-cowpea intercrop with cowpea planted 20 cm outside the maize basin. There was significant difference (P < 0.001) in RLD, grain yield and stover yield. Maize-cowpea intercropped within the same basin achieved higher RLD, grain yield and stover yield than cowpea that was intercropped outside the basin and the sole crops. The land equivalent ratio (LER) in both intercrop designs showed that intercropping had better grain yield performance when compared to sole cropping. It can be concluded that intercropping maize and cowpeas within the same basin can result in an environment around the crop achieving higher RLD which translates to better grain yield compared to the sole cropping and intercropping cowpeas outside the basin.

丙酰芸苔素内酯施用浓度对水稻植株性状和产量的影响

为了明确丙酰芸苔素内酯对水稻植株性状和产量的作用,采用单因素拉丁方设计,试验因素为0.003%丙酰芸苔素内酯水剂施用浓度,设4个处理,处理A稀释500倍液,处理B稀释2 000倍液,处理C稀释3 000倍液,处理D稀释4 000倍液,设喷施等量清水空白对照(CK),每个处理5次重复。收获前调查记录植株相关性状和产量构成因子,每个重复单独收获脱粒烘干测产。结果表明,水稻移栽后,丙酰芸苔素内酯稀释2 000倍液叶面喷施2次,植株高度为100.9 cm,分蘖数为23.0,穗下节间、倒2节间和倒3节间的长度分别为22.3、19.7和16.4 cm,每穗总粒数、实粒数和千粒重分别为137.2粒、128.9粒和32.1 g,产量为7 362.7 kg/hm~2。因此,0.003%丙酰芸苔素内酯水剂稀释2 000倍液可增加水稻植株高度、节间长度、分蘖数和提高产量。

Influence of Topological Properties of Complex Networks on the Effect of Spectral Coarse-Grained Network

Recently, some coarse-graining methods based on network synchronization have been proposed to reduce the network size while preserving the synchronizability of the original network. In this paper, we investigate the effects of the coarse graining process on synchronizability over complex networks under different average path lengths and different degrees of distribution. A large amount of experiments demonstrate a close correlation between the average path length, the heterogeneity of the degree distribution and the ability of spectral coarse-grained scheme in preserving the network synchronizability. We find that synchronizability can be well preserved in spectral coarse-grained networks when the considered networks have a longer average path length or a larger degree of variance.