Genome-wide Association Analysis of Rice Heading Date and Yield-related Traits Based on MAGIC Population

【Objective】The objective of the study is to identify new genes related to heading date and yield related traits in rice, and to screen the elite rice lines carrying favorable alleles, therefore providing new genes and excellent germplasm for molecular marker-assisted (MAS) breeding.【Method】The multi-parent generation inter-crosses (MAGIC) population MAGIC-Hei was planted in 2017 and 2018 in Changsha, Hunan Province. Genome-wide association analysis was performed to detect the quantitative trait loci associated with heading date, number of tillers per plant, grain number per panicle, seed setting rate, 1000-grain weight and grain yield per plant based on genotyping by sequencing (GBS).【Results】Totally, 26 QTLs that control heading date and yield related traits were identified on all the chromosomes except chromosome 10 in the two years. Of these, 11 are new and qNTP9, associated with the number of effective panicles, was detected in the two years. qNTP9 was less affected by environment and could be used for further fine mapping and gene cloning. Based on the phenotypic and the SNP genotypes five elite lines carrying favorable alleles were selected, which could be used for future high-yielding rice breeding. 【Conclusion】The loci associated with heading date and yield related traits could be used for rice breeding.     

杂交籼稻外观品质性状与食味品质性状典型相关分析

为了明确稻米外观品质与食味品质的关系,甄选合适的评价指标,为培育外观品质与食味品质综合优良的杂交籼稻品种提供理论参考,以8个不育系与25个恢复系配制的200个杂交籼稻组合为材料,采用简单相关和典型相关分析研究了稻米外观品质性状与食味品质性状的相关关系。结果表明,直链淀粉含量与粒宽、垩白度、垩白粒率呈显著正相关,与长宽比显著负相关;米饭食味综合评分与粒长、长宽比显著正相关,与粒宽显著负相关。典型相关分析得到相关系数达显著水平的两对典型相关变量,累计贡献值为91.329%。在第一对典型变线性组合构成中,U₁和V₁分别以长宽比、直链淀粉含量的权重较大;在第二对典型变线性组合构成中,U₂和V₂分别以粒长、食味综合评分的权重较大。     

应用CRISPR/Cas9技术与分子标记辅助选择创制广东丝苗米新种质

【目的】创制优质香型丝苗米水稻新种质，探索水稻育种改良新途径，助力广东丝苗米品牌建设。【方法】以广东省农业主导品种粤农丝苗(YNSM)与优质稻粤王丝苗(YWSM)为材料，利用CRISPR/Cas9基因编辑技术定点编辑上述品种的香味基因Badh2，创制香稻新品系，随后通过分子标记辅助选择(MAS)技术定向导入GW7/GL7位点，系谱选育优质香型丝苗米水稻新种质。【结果】利用CRISPR/Cas9基因编辑技术成功创制两个香稻新品系yn-ko^badh2与yw-ko^badh2，其2-AP含量均极显著提高，达到239.39～440.79μg/kg，而有效穗数、每穗实粒数、糙米外观品质、千粒重与产量等主要农艺性状均未受到显著影响；MAS技术结合系谱选育的方法成功选育两个丰产性好、籽粒长宽比超过4.3的优质香型丝苗米水稻新品系NW^badh2GW7-1与NW^badh2GW7-2，达到广东丝苗米品种关于香味与外观粒型的认定标准。【结论】利用CRISPR/Cas9基因编辑与分子辅助选择技术相结合可精准、高效地创制新的优...     

Genome-Wide Association Analysis and Allelic Mining of Grain Shape-Related Traits in Rice

Excavating single nucleotide polymorphisms(SNPs) significantly associated with rice grain shape and predicting candidate genes through genome-wide association study(GWAS) can provide a theoretical basis for discovery and utilization of excellent genetic resources in rice. Based on 16 352 SNPs, 161 natural indica rice varieties with various grain sizes in southern China were used for GWAS of grain shape-related traits, referring to grain length(GL), grain width(GW), 1000-grain weight(TGW), and grain length/width(GLW). Phenotypic statistics showed that coefficient of variation values for these four traits GL, GW, TGW and GLW were 9.92%, 9.09%, 20.20% and 16.38%, respectively. Each trait showed a normal distribution, and there was a certain correlation between these traits. Through general linear model correlation analysis, a total of 38 significant loci were identified, and a range of 100 kb upstream and downstream of the significant loci was identified as the candidate interval. On chromosome 3, GS3 and q GL3 were found to regulate GL. On chromosome 6, TGW6 and GW6 a were found to regulate TGW. Also, some QTLs related to grain shape were found on chromosomes 5 and 9. Besides that, using sequenced 3 K-germplasm resources, we found that there are 22 overlapped varieties between these two natural populations. Twenty-six SNPs and fourteen haplotypes were identified in five regions of GS3 genes. The detection of multiple candidate genes/QTLs within the candidate interval is beneficial for further excavation of superior rice genetic resources.     

杂交稻米质性状的亲本配合力分子标记鉴定

摘要: 利用水稻微卫星分子标记技术,结合半双列杂交方法,对F1的米粒长宽比、精米千粒重、垩白度、碱消值、胶稠度等5个主要米质性状进行了亲本配合力分子标记研究,结果获得了与这些性状极显著相关的18个亲本微卫星分子标记,其中,米粒长宽比4个,精米千粒重3个、垩白度4个、碱消值4个、胶稠度3个。这些标记可以直接用于杂种米质预测和亲本的分子辅助育种改良。同时,进行了亲本与F1在这些性状上的相关分析。相关分析结果表明在米粒长宽比和精米千粒重两个性状上,恢复系和不育系对F1的相关系数都很接近。然而在垩白度、碱消值和胶稠度上,母本对F1的相关系数显著大于父本,表现出母性遗传特点。     

多环境下大豆子粒大小性状的全基因组关联分析

为探究多环境下大豆子粒大小性状的分子遗传基础,挖掘与子粒大小性状相关的SNP位点和候选基因,利用150份大豆种质资源在2019年和2020年6个环境条件下对大豆子粒粒长、粒宽、粒厚和百粒重性状进行表型测定,并进行全基因组关联分析。结果表明：在CMLM（压缩混合线性）模型下,在6个环境条件下检测到896个与子粒大小性状显著关联的SNP位点,分布于20条染色体。不同性状检测到72个重叠的SNP位点。检测到39个稳定遗传的SNP位点,贡献率为10.68%~24.93%。通过稳定性与重叠性分析,获得35个稳定表达的SNP位点,贡献率为10.92%~23.16%。在粒宽、粒厚及百粒重性状中同时检测到显著关联的SNP位点最多,位点rs16533609的贡献率最高（16.51%）。根据稳定表达的SNP筛选候选基因,推测Glyma.03G006600、Glyma.04G077100、Glyma.08G203600、Glyma.12G195400、Glyma.17G039800、Glyma.18G202100和Glyma.20G215700等7个基因对大豆子粒大小性状有调控作用。     

Effect of Cold-Water Irrigation on Grain Quality Traits in japonica Rice Varieties from Yunnan Province, China

The response of grain quality traits to cold-water irrigation and its correlation with cold tolerance were studied in 11 japonica rice varieties from Yunnan Province, China. The results indicated that the response of grain quality traits to the cold-water stress varied with rice varieties and grain quality traits. Under the cold-water stress, grain width, chalky rice rate, whiteness, 1000-grain weight, brown rice rate, taste meter value, peak viscosity, trough viscosity, breakdown viscosity and final viscosity significantly decreased, whereas grain length-width ratio, head rice rate, alkali digestion value, protein content and setback viscosity markedly increased. However, the other traits such as grain length, amylose content, milled rice rate, peak viscosity time and pasting temperature were not significantly affected by the cold-water stress. Significant correlations were discovered between phenotypic acceptability and cold response indices of taste meter value, protein content, peak viscosity and breakdown viscosity. Therefore, it would be very important to improve the cold tolerance of Yunnan rice varieties in order to stabilize and improve their eating quality.     

Genome-Wide Association Studies Reveal New Genetic Targets for Five Panicle Traits of International Rice Varieties

Narrow genetic background is a key limiting factor in breeding stable high-yielding rice. The introduction and utilization of international rice core germplasm is an important way to increase the genetic diversity of domestic rice varieties. We conducted a genome-wide association study on 5 panicle traits of 315 rice accessions introduced from the international rice micro-core germplasm bank. Based on the tests from Yangzhou of China and Arkansas of American, environment exhibited a significant impacts on panicle length and primary branch number, while grain length, grain width and grain length/width ratio were insensitive to environment changes. We discovered a total of 7, 5, 10, 8 and 6 chromosomal regions or single nucleotide polymorphism marker loci that were significantly associated with primary branch number, panicle length, grain length, grain width and grain length/width ratio, respectively. Among them, eleven regions were associated with grain shape and one region associated with primary branch number, showing the good consistence in two different environments. Significant linear correlation was discovered between the average trait value and the number of favorable alleles carried by the varieties in all associated loci. Among the associated loci, varieties in aromatic and tropical japonica sub-groups possessed most favorable alleles, while those in temperate japonica sub-group contained the least. The domestic varieties mainly harbored unfavorable alleles in six of the associated loci being detected. On the contrary, 15 varieties from 11 different countries harbored more favorable alleles(as many as 30 or more) than the others. Remarkably, all these 15 varieties belonged to the tropical japonica sub-group. In conclusion, our study demonstrates that varieties in the tropical japonica sub-group had high potentials for breeding stable high-yielding rice. Based on this discovery, we proposed a new approach for improving the panicle traits of domestic rice by using tropical japonica varieties.     

水稻粒宽突变体gw4的鉴定与基因定位

[目的]水稻粒形是影响水稻产量和决定稻米外观品质的主要性状之一.筛选和鉴定新的粒形突变材料,可为研究水稻籽粒发育的调控机制奠定基础.[方法]粳稻品种中花11经1％的EMS处理,在诱变群体中获得一份窄粒突变体gw4(grain width on chromosome 4);分析粒形和其他主要农艺性状,在扫描电镜下观察颖壳...     

Association mapping of grain quality and flowering time in elite japonica rice germplasm

Grain quality traits play an important role in the economic prosperity of commercial rice markets. The objective of our research was to identify candidate molecular markers associated with three grain quality and flowering traits in a collection of elite rice japonica inbred lines evaluated in five U.S. states. Candidate marker effects were associated with the traits mapped within regions reported from previous QTL analyses while several new allelic interactions were also detected. Common markers for each trait were observed across two or more locations, and two-way interactions unique to a single location were also found. Significant genotype × location interactions were detected while broad-sense heritability estimates were low for all characters. All but one selected marker effect was associated with a reduction in apparent amylose content. A reduction in heading date at three locations was observed with one marker as a main effect or as a component of two-way interactions that mapped ∼ 5 cM from the Hd3a flowering locus. The majority of selected effects for head rice were associated with modest to substantial increases in value. Marker loci and their interactions identified in this study highlighted targeted regions for future association studies and marker-assisted breeding efforts of grain quality traits.     

利用CRISPR/Cas9技术高效创制长粒香型水稻

【目的】CRISPR/Cas9基因编辑技术已成为水稻分子育种的重要手段。为了促进水稻育种的发展,本研究以非香型粳稻品种龙粳11为试验材料,对GS3、GS9和Badh2基因进行编辑,以期获得能稳定遗传的长粒香水稻材料。【方法】利用CRISPR/Cas9技术,以GS3、GS9和Badh2为靶基因,构建敲除载体pYLCRISPR/Cas9-GS3/ GS9/Badh2-gRNA,通过农杆菌介导法,在龙粳11的GS3、GS9和Badh2基因中引入了特定的突变。【结果】T₂代无转基因的gs3/gs9/badh2纯合突变体与野生型龙粳11相比,粒长增加26.43%~27.01%,单株产量增加10.82%~12.11%,千粒重增加18.34%~41.36%,稻米变香,高效地将圆粒水稻变成长粒香型水稻。【结论】利用CRISPR/Cas9技术获得能够稳定遗传并具有长粒香品质的纯合突变株系,为组合多个品质性状提供了一种方便有效的方法,从育种角度加快了新品系创制过程。     

大麦籽粒大小的遗传多样性与稳定性评价

为了解大麦籽粒大小的遗传多样性与稳定性,以185份大麦种质资源为材料,测定了7个试验环境下籽粒的长度、宽度、长宽比及千粒重等性状,对其遗传多样性和稳定性进行了分析评价。结果表明,所有试验环境下二棱大麦粒长、粒宽及千粒重均值均大于六棱大麦,籽粒长宽比均值均小于六棱大麦;二棱大麦与六棱大麦千粒重、粒长、粒宽及籽粒长宽比在品种(系)间及环境间差异均极显著,且品种(系)与环境之间存在极显著的互作效应,籽粒大小在环境间差异程度因性状而异,其中以千粒重的差异程度最大。依据10级分类分布频次法则,千粒重和粒宽分布比较集中,六棱大麦集中分布在3、4等级,二棱大麦集中分布在7、8等级;粒长和籽粒长宽比分布比较分散,六棱大麦粒长和籽粒长宽比分别分布在1~10等级和2~10等级范围内,二棱大麦粒长和长宽比分别集中分布在4~8等级和2~7等级范围内。千粒重与粒长、粒宽及粒长与籽粒长宽比呈极显著正相关,粒宽与籽粒长宽比呈极显著负相关;粒长与粒宽及千粒重与籽粒长宽比的相关性因棱型不同而异。二棱大麦千粒重的稳定性小于六棱大麦,而粒长和籽粒长宽比的稳定性恰好相反,粒宽的稳定性与棱型无关;皮大麦千粒重稳定性小于裸大麦,其余籽粒大小性状的稳定性与皮裸无关。通过熵权法TOPSIS对大麦籽粒大小进行综合评价,筛选出籽粒饱满且稳定的品种川52209,其可作为大麦籽粒性状改良的优异种质。     

水稻特大粒种质BG1和优质恢复系华占的粒形基因研究及相关功能标记开发

【目的】特异种质资源的发掘与利用是水稻优质高产育种的重要手段之一。明确特大籽粒种质BG1（Big Grain 1）和育种上广泛配组的优质恢复系华占携带的部分粒形基因等位变异类型,并开发相应基因的功能标记,有助于加快粒形基因的育种应用,提高水稻粒形精准改良的效率。【方法】对BG1和华占中的9个主效粒形基因（GS3、qLGY3、qGL3、GW2、GW8、GW5、TGW3、TGW6、GS9）的目的片段进行测序分析。并根据GW2、GS3、qGL3、TGW3、TGW6、qLGY3、GW8和GW5的测序结果,开发了鉴定其基因分型的功能标记。【结果】与日本晴相比,特大粒种质BG1在检测的9个主效粒形基因中有5个表现为功能缺失型（gs3、GW8、gw2、tgw3、tgw6）,1个稀有等位变异（qgl3）和1个外显子可变剪切型（qlgy3）;与日本晴相比,华占在检测的9个主效粒形基因中有3个（gs3、GW8、GW5）存在差异。根据测序结果开发了GW2、GS3、qGL3、TGW3、TGW6、qLGY3、GW8和GW5的功能标记,并利用15个水稻种质进行检测,检测结果中除了TGW6 的标记TGW6-Del 仅可用于鉴定是否含有功能缺失型的等位变异tgw6外,另外7个标记均为可准确鉴定基因型。【结论】与日本晴相比,特大粒种质BG1中调控粒长的基因gs3、qgl3、qlgy3、tgw3、GW8和tgw6之间可能存在复杂的互作调控通路,而不是简单的效应累加,粒宽特征可能是gw2、GW8的累加效应。优质恢复系华占的细长粒形可能是gs3、GW5和 GW8的互作效应所致。本研究中开发的功能标记可以用于水稻分子标记辅助育种。     

水稻粒重及其相关性状的遗传解析

 应用292个 Lemont/ 特青F13重组自交系(RILs)和272个标记的遗传连锁图谱分析粒重及籽粒长、宽、厚、长/宽、体积和容重6个相关性状的遗传。所有性状在RILs中出现超亲分离。粒重与其他籽粒性状均呈显著正相关，而涉及籽粒品质的容重与粒宽、粒厚呈显著负相关。检测到影响粒重及其相关性状的主效QTL 48个和互作位点38对，这些QTL解释了各性状55%以上的表型变异。80%以上的主效QTL呈现一因多效或生理相关。QGl3和 QGl2等通过籽粒体积间接影响粒重， Lemont增效等位基因有利于籽粒品质的改良，而QGw5、QGt1和QGv7的特青增效等位基因增加粒重同时降低籽粒容重及品质。通过标记辅助选择进行不同QTL的重组，有望在增加粒重的同时改善籽粒品质。     

不同生态地点下稻米外观品质性状的QTL定位分析

 利用两个已测序品种93 11和日本晴为亲本,采取单粒传法创建由190个家系组成的重组自交系群体,并构建了包含178个SSR、CAP和STS标记的遗传连锁图谱。采用复合区间作图方法,在3个不同生态地点(陵水、合肥和怀远)对垩白(垩白率、垩白大小、垩白度)、粒形(粒长、粒宽、长宽比)等6个外观品质的数量性状基因座（QTL)进行了定位分析。共定位到39个QTL,单个性状QTL数目在6~7个,说明垩白和粒形是多基因控制的数量性状。8个QTL可在2个以上地点检测到,其中,两个垩白度相关QTL qCD 1、qCD 3(贡献率分别为288%、321%)在3个地点同时检测到;11个QTL具有一因多效性,单个QTL位点控制的性状为2~6个,如第3染色体RM16-RM143区段控制垩白率、垩白大小、垩白度、粒长、粒宽和长宽比等6个性状。比较3个地点的检测结果,发现外观品质性状的QTL定位都受环境影响,但不同性状受影响的程度不同。长宽比和垩白度受环境影响较小,粒宽受环境影响较大。     

水稻粒宽基因GS5的功能标记开发和单倍型鉴定

水稻粒宽是影响籽粒粒形的重要因素之一,也是一个与水稻产量和稻米品质密切相关的重要性状。在基因GS5序列分析的基础上,对该基因第2外显子的ACC/CTA和第9外显子A/C的两个变异位点分别开发了功能标记,并将其用于294份水稻微核心种质和2007-2013年江苏省审定的65份粳稻品种的基因型鉴定。研究结果表明,这两个变异位点的等位变异在水稻籽粒的粒长、粒宽和长宽比性状上存在显著或极显著的差异;其在水稻微核心种质中组成的4种单倍型在水稻籼亚种的粒宽、粒厚和长宽比性状上存在极显著的差异,在粳亚种的粒宽和长宽比性状上存在极显著的差异;而江苏省审定的粳稻品种中仅发现Hap1和Hap2两种单倍型,其分别有64个和1个代表性品种。这些研究结果为水稻产量和稻米品质育种中充分利用GS5的优异等位基因或单倍型奠定了基础。     

二棱大麦与六棱大麦籽粒性状的差异性及其相关性

为了解不同棱型大麦籽粒性状的差异性及其千粒重与粒型性状的相关性,对98份二棱大麦和89份六棱大麦品种(系)在不同试点的千粒重、粒长、粒宽进行测定和分析。结果表明,二棱大麦千粒重、粒长和粒宽普遍高于六棱大麦,不同棱型大麦千粒重、粒长和粒宽在基因型间及环境间差异均达到显著或极显著水平。经过聚类分析,依据千粒重将二棱大麦和六棱大麦聚为高、中、低粒重3类。随着千粒重的减小,二棱大麦千粒重与粒长之间由显著正相关变为不显著负相关,六棱大麦则由不显著正相关变为显著正相关。二棱大麦和六棱大麦各类品种(系)的平均千粒重与粒宽均呈极显著正相关,而且相关系数均高于千粒重与粒长的相关系数。     

Association Mapping of Quantitative Trait Loci for Grain Size in Introgression Line Derived from Oryza Rufipogon

Grain size is one of the critical agronomic traits governing grain yield and quality in rice. However, the underlying genetic mechanisms that control grain size in rice are poorly understood. We used an introgression line derived from Zhonghui 8015 and Oryza rufipogon Griff. This introgression line was evaluated under two different environmental conditions to dissect the quantitative trait loci controlling grain size. Genome-wide association study (GWAS) was performed using 28 193 SNPs through a general linear model, and 56 significant SNPs on different loci associated with the 4 grain size traits were detected. Cloned genes including GS3 and qGL3 showed substantial effects on grain length and size. Seven new stable loci were identified with pleiotropic effects on grain size. Haplotype, gene expression analyses, combined gene-based associations, and functional annotations permitted the shortlisting of important dominant genes including GS3 and qGL3.     

旱稻数量性状的遗传参数分析

从广义遗传力、遗传相关、遗传进度和选择指数等几个方面,分析了57份旱稻品种的株高、有效穗数、主穗长度、主穗粒数、千粒重、单株粒重和剑叶长/宽7个主要数量性状的遗传潜力和选择效果.分析结果表明：株高、剑叶长/宽、单株粒数、主穗长度、千粒重的广义遗传力较高,有效穗数、单株粒重的广义遗传力偏低;单株粒数、单株粒重、有效穗数3个主要产量构成因素的遗传变幅较大,在该群体中对这3个性状进行选择的潜力较大;产量性状中的单株粒数和千粒重与单株粒重本身均有一定的遗传潜力,预期遗传进度也较大,特别是单株粒数的预期遗传进度较大;单株粒重与单株粒数、千粒重间存在显著或极显著的遗传正相关,主穗长度与有效穗数间存在极显著的遗传负相关,因此可以通过提高单株粒数和千粒重来间断增加单株产量;用单株粒重与单株粒数、千粒重和有效穗数构成的选择指数进行综合选择,相对效率高达219.34%,比直接选择单株粒重提高了119.34%,显著高于对单株粒重的直接选择,因此采用这个指数对单株粒重进行间接选择效果较为理想.     

黄淮麦区部分小麦品种(系)重要产量性状全基因组关联分析

为挖掘与小麦产量性状的相关等位变异及给分子标记辅助育种提供参考,选取SSR与SNP标记对52个黄淮麦区品种(系)材料进行全基因组扫描,对株高、穗长、单株穗数、可育小穗数、穗粒数、千粒重等6个重要产量性状进行标记,并进行遗传多样性、群体遗传结构与全基因组关联定位等分析。结果表明,供试群体可被划分为4个亚群,5种环境间所测产量性状差异均达到0.05显著水平,且穗长和单株穂数的变异系数最大。利用Powermarker进行标记遗传多样性分析,共检测到899个等位变异,平均等位变异丰富度为3.625,遗传多样性指数平均值为0.586,多态性信息含量(PIC)平均值为0.510。利用Tassel的MLM(Q+K)模型关联得到与产量显著关联的分子标记共13个(6个SSRs和7个SNPs),这些与产量相关性状的优异等位变异可为发掘和利用小麦育种优良基因提供依据,并为今后的遗传育种工作提供参考。