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.

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.

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.

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.

玉米亲本自交系及杂交种机械粒收质量相关指标分析

以玉米亲本自交系及杂交种为试验材料,于2019—2020年对玉米植株地上倒3—5节的折断力、节间长、节间粗及收获时籽粒含水率、破碎率、抗压能力、脱水速率等指标进行分析,并筛选茎秆强度强、籽粒机收质量好的玉米材料,为适宜机械粒收玉米新种质的培育奠定基础。结果表明,自交系E8501和杂交种郑单6122的茎秆折断力较大,自交系郑58、ZC1456和杂交种郑单958折断力较小;自交系郑682和杂交种先玉335的节间较长,自交系郑588和杂交种郑单1002的节间较短;自交系郑P6、PH6WC和杂交种DK517节间较粗,自交系郑682和杂交种郑单6098节间较细。聚类分析结果表明,玉米亲本自交系E8501、郑7541、郑H71、郑V89M、郑D58M、HCL1645和PH4CV及杂交种郑单6386、郑单6122、DK517、郑单6095、郑单6098、郑单1868和郑单1002的茎秆强度较强。杂交种郑单958的籽粒含水率较高,郑单6122较低;自交系郑H71和杂交种郑单958、郑单1868的籽粒破碎率较高,自交系PH4CV和杂交种DK517的籽粒破碎率较低;自交系PH4CV和杂交种郑单6122的籽粒抗压能力较大,自交系郑H71和杂交种郑单958的籽粒抗压能力较小。玉米收获时籽粒含水率≤26.87%就能够满足籽粒破碎率≤5%的机械粒收标准。在上述14个抗倒伏能力较强的玉米材料基础上,最终筛选出亲本自交系E8501、郑7541、郑H71、郑V89M、郑D58M、HCL1645和PH4CV以及杂交种DK517、郑单6122、郑单6386和郑单6098为抗倒伏较强且机械粒收质量佳(籽粒含水率≤26.87%且破碎率≤5%)的材料。

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。

基于水稻矮秆长粒CSSL-Z688的QTL鉴定及SSSLs培育

水稻株高、粒型等性状是由多基因控制的数量性状,遗传基础复杂.水稻染色体片段代换系(CSSL)是研究复杂性状的理想遗传材料,然而目标基因的水稻单片段代换系(SSSL)的培育则需要多年多代逐步完成.以4代换片段的水稻矮秆长大粒CSSL-Z688为研究材料,鉴定出7个株高及粒型性状的数量性状基因座(quantitative trait locus,QTL);进一步培育了目标QTL的5个纯合单片段代换系和5个杂合单片段代换系,其中6个QTLs(qPH1-1,qPH1-2,qGL1,qGL12,qRLW1和qGWT1)能够被纯合单片段代换系所验证.还鉴定出11个新QTLs,分别为qPH2,qGL1-2,qGL2,qGW1,qRLW1-2,qRLW2,qRLW12,qGWT1-2,qGWT2,qGWT6和qGWT12,其中7个QTLs尚未被报道.QTL加性和显性效应表明:水稻株高、粒长、千粒质量等表型同时受到多个QTL加性和显性效应的共同影响,如来自供体西恢18的qph1-1,qPH1-2,qPH2的加性效应和qPH1-1/qph1-1及qPH1-2/qph1-2和qPH2/qph2的显性效应共同影响株高的遗传;来自西恢18的qGL1,qgl1-2,qGL2和qGL12的加性效应及qGL1/qgl1的显性效应共同影响水稻粒长的遗传;来自西恢18的qGWT1,qGWT1-2,qGWT2,qGWT6和qGWT12的加性效应及qGWT1/qgwt1,qGWT1-2/qgwt1-2,qGWT6/qgwt6,qGWT2/qgwt2和qGWT12/qgwt12的显性效应共同影响千粒质量的遗传.这些结果表明单片段代换系的构建可有效地将遗传复杂的数量性状分解为单位点进行研究,为以单片段代换系为平台的水稻分子设计育种提供了重要遗传信息.

青稞籽粒长和宽的差异性

为了解青稞籽粒长、宽在品种(系)间的差异,以来自国内外的214份青稞品种(系)为材料,对粒长、粒宽进行鉴定分析。结果表明,青稞粒长、粒宽在品种(系)间均存在显著差异。粒长的变异范围为4.125~8.117 mm,平均值6.075 mm,总变异系数10.906%;籽粒较长的材料有北青2号(青海海北)、长芒裸大麦(云南昆明)、白青稞(西藏隆子)、山青7号(西藏山南)和喜马拉4号(西藏仁布),以喜马拉4号最长;籽粒较短的材料有湟中六棱青稞(青海湟中)、扎骨(西藏左贡)、褐青稞(青海)、米大麦(云南晋宁)和米如红(西藏南木林),以湟中六棱青稞最短。粒宽变异范围为1.670~3.553 mm,平均值2.596 mm,总变异系数13.721%;籽粒较窄材料有米如红(西藏南木林)、白青稞(西藏昌都)、丹巴黑青稞(四川丹巴)、冬207(西藏拉萨)和白青稞(西藏隆子),其中最窄品种为米如红;较宽材料为Bang-Iu(墨西哥)、紫青稞(西藏穷结)、繁29(青海)和喜马拉6号(西藏日喀则),最宽材料为喜马拉6号。从材料来源看,青稞粒长在不同地区间也差异显著,但粒宽差异不显著;甘肃材料的粒长平均值最大(6.273 mm),云南材料的最低(5.737 mm);最大值(8.117 mm)出现在西藏材料中,最小值(2.560 mm)在青海材料中。粒宽以来自国外的材料平均值最高(2.744 mm),云南材料的平均值最低(2.315 mm),最大值(3.553 mm)与最小值(1.670 mm)均出现在西藏材料中。通过聚类分析,根据粒长将214份材料聚类可分为较长粒型、较短粒型、短粒型和长粒型四类;根据粒宽也可划分为较宽粒型、宽粒型、窄粒型和较窄粒型四类;综合粒长和粒宽筛选出四个大粒品种(系)即拉萨蓝青稞(西藏拉萨)、奶玛(西藏波密)、北青2号(青海海北)和长芒裸大麦(云南昆明)。

缺失OSR结构域功能的GS3蛋白正向调控水稻籽粒大小

水稻种子粒型是影响产量的重要因素。GS3基因是水稻第一个被克隆的粒型基因,主要调控籽粒的粒长和粒重。GS3蛋白包含N端的OSR(Organ size regulation)和C端的Cys-rich功能结构域。GS3基因主要存在4种自然变异类型,分别为GS3-1至GS3-4。其中,GS3-1编码全长GS3蛋白;GS3-2编码的蛋白质插入1个氨基酸;GS3-3导致GS3完整蛋白缺失,表现为籽粒变长;GS3-4编码N端的OSR结构域,表现为籽粒明显变短。截至目前,在水稻自然变异中仍未发现仅编码C端的Cysrich结构域的GS3变异类型,其对籽粒大小的调控也不清楚。本研究利用CRISPR/Cas9基因编辑技术在DNA序列两侧设计靶点删除大片段序列,创制出仅编码C端Cys-rich功能结构域的突变类型gs3-5,并获得纯合突变株系。与受体背景中花11相比,gs3-5纯合突变株系表现为粒长和千粒重增加。上述结果表明OSR结构域是GS3蛋白作为籽粒大小的负调控因子所必需的,为进一步解析OSR结构域对籽粒大小的调控以及探索新的育种改良方法提供了参考。

散装储粮平房仓水平联梁间墙体计算长度取值探讨

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