Genome-Wide Association Study of Nitrogen Use Efficiency and Agronomic Traits in Upland Rice

Genome-wide association study (GWAS) was performed for 16 agronomic traits including nitrogen use efficiency (NUE) and yield-related components using a panel of 190 mainly japonica rice varieties and a set of 38 390 single nucleotide polymorphism (SNP) markers. This panel was evaluated under rainfed upland conditions in Madagascar in two consecutive cropping seasons with two contrasted nitrogen input levels. Using another set of five grain traits, we identified previously known genes (GW5, GS3, Awn1 and Glabrous1), thus validating the pertinence and accuracy of our datasets for GWAS. A total of 369 significant associations were detected between SNPs and agronomic traits, gathered into 46 distinct haplotype groups and 28 isolated markers. Few association signals were identified for the complex quantitative trait NUE, however, larger number of quantitative trait loci (QTLs) were detected for its component traits, with 10 and 2 association signals for nitrogen utilization efficiency and nitrogen uptake efficiency, respectively. Several detected association signals co-localized with genes involved in nitrogen transport or nitrogen remobilization within 100 kb. The present study thus confirmed the potential of GWAS to identify candidate genes and new loci associated with agronomic traits. However, because of the quantitative and complex nature of NUE-related traits, GWAS might have not captured a large number of QTLs with limited effects.     

Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study

Sheath blight (SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci (QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study (GWAS) of SB resistance using 299 varieties from the rice diversity panel 1 (RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism (SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica (TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.     

Genetic Dissection of Grain Size Traits Through Genome-Wide Association Study Based on Genic Markers in Rice

Grain size plays a significant role in rice, starting from affecting yield to consumer preference, which is the driving force for deep investigation and improvement of grain size characters. Quantitative inheritance makes these traits complex to breed on account of several alleles contributing to the complete trait expression. We employed genome-wide association study in an association panel of 88 rice genotypes using 142 new candidate gene based SSR (cgSSR) markers, derived from yield-related candidate genes, with the efficient mixed-model association coupled mixed linear model for dissecting complete genetic control of grain size traits. A total of 10 significant associations were identified for four grain size-related characters (grain weight, grain length, grain width, and length-width ratio). Among the identified associations, seven marker trait associations explain more than 10% of the phenotypic variation, indicating major putative QTLs for respective traits. The allelic variations at genes OsBC1L4, SHO1 and OsD2 showed association between 1000-grain weight and grain width, 1000-grain weight and grain length, and grain width and length-width ratio, respectively. The cgSSR markers, associated with corresponding traits, can be utilized for direct allelic selection, while other significantly associated cgSSRs may be utilized for allelic accumulation in the breeding programs or grain size improvement. The new cgSSR markers associated with grain size related characters have a significant impact on practical plant breeding to increase the number of causative alleles for these traits through marker aided rice breeding programs.     

337份小麦品种籽粒相关性状的全基因组关联分析

小麦籽粒大小和形态是决定产量的主要因素之一,挖掘籽粒相关性状的关联位点,筛选相关候选基因为提高小麦产量奠定了重要基础。本研究以337份小麦品种作为研究对象,利用Q+K混合线性模型(MLM)在3个环境(E1:2020年陕西杨凌;E2:2020年陕西斗口;E3:2021年陕西杨凌)下对小麦的千粒重、粒长、粒宽以及籽粒长宽比4个性状进行了全基因组关联分析(GWAS)。在3种环境中,不同小麦品种的4个籽粒性状都表现出了广泛的表型差异,变异系数为5.31%～14.76%,其中粒长的变异幅度最小,千粒重的变异幅度最大。GWAS结果表明,49个显著SNP位点至少在2个环境中被检测到,分布在除1B、4A和7D外的染色体上,解释了3.36%～12.73%的表型变异。检测到一因多效位点31个,在5A染色体上检测到3个环境下与3个籽粒性状(千粒重、粒长、粒宽)稳定相关的位点,表型贡献率为3.51%～7.74%。对稳定关联的SNP位点上下游各200 kb的物理区间内进行候选基因挖掘,筛选到5个(TraesCS2B01G225400、TraesCS4D01G016900、TraesCS5A01G454100、T...     

超级杂交稻协优9308重组自交系群体的穗部性状QTL分析

 将281个株系组成的超级杂交稻协优9308重组自交系群体种植在海南陵水（2006年和2007年）和浙江富阳（2006年）,采用Windows QTL Cartographer 2.5的复合区间作图法进行QTL检测。共检测到控制7个穗部性状的52个QTL,其中包括7个控制穗长的QTL,8个控制一次枝梗数的QTL,9个控制二次枝梗数的QTL,6个控制着粒密度的QTL, 7个控制每穗总粒数的QTL,11个控制每穗实粒数的QTL,4个控制结实率的QTL。单个QTL对群体性状表型变异的贡献率为23%~312%。控制穗部性状的QTL基本上以加性效应为主,上位性效应和环境互作效应不大。在3组试验中都检测到控制3个穗部性状的8个QTL：qPL-1,qPL-6-1;qTNSP-1,qTNSP-2,qTNSP-3;qNFGP-1,qNFGP-3-2,qNFGP-6-2。这些QTL,尤其是第3染色体RM168-RM143区间控制每穗总粒数的qTNSP-3和控制每穗实粒数的qNFGP-3-2,其加性效应值和贡献率均较大,可以考虑下一步进行QTL精细定位和克隆。研究发现多个重要QTL聚集区间,在同一QTL聚集区间,控制相关性状的QTL效应方向基本上相同,利用这些QTL紧密连锁的分子标记进行辅助选择,可望同时针对多个性状进行遗传改良。     

转Bt基因水稻克螟稻杂交转育后代农艺性状的研究

 对转Bt基因水稻与常规品种的杂交后代进行了GUS活性的组织化学分析和农艺性状考察。结果表明，报告基因gus与抗虫基因 cry1Ab是连锁遗传和协同表达的，利用GUS组织化学染色法可快速筛选抗虫杂种植株；无论是籼粳交，还是粳粳交后代，抗虫和感虫的两类植株间在株高、穗长、单株分蘖数、播始历期和千粒重等主要农艺性状上无显著差异，这无疑为利用Bt水稻培育优良的抗虫品种提供了科学依据。     

Novel Sources of aus Rice for Zinc Deficiency Tolerance Identified Through Association Analysis Using High-Density SNP Array

Zinc (Zn) deficiency is a major soil constraint limiting rice crop growth and yield, yet the genetic control of tolerance mechanisms is still poorly understood. Here, we presented promising loci and candidate genes conferring tolerance to Zn deficiency and identified through association analysis using a 365 K single nucleotide polymorphism (SNP) marker array in a diverse aus (semi-wild type rice) panel. Tolerant accessions exhibited higher growth rate with relatively rare stress symptoms. Two loci on chromosomes 7 and 9 were strongly associated with plant vigor under Zn deficiency at a peak-stress stage. Based on previous microarray data from the same experimental plots, we highlighted four candidate genes whose expressions were accompanied by significant genotype and/or environment effects under Zn deficiency. Network-gene ontology supported known tolerance mechanisms, such as ascorbic acid pathway, and also suggested the importance of photosynthesis genes to overcome Zn deficiency symptoms.     

New Stably Expressed Loci Responsible for Panicle Angle Trait in Japonica Rice in Four Environments

Panicle angle (PA) of 254 recombinant inbred lines derived from a cross between two japonica varieties Xiushui 79 and C Bao was investigated under four environments,and a genetic linkage map including 111 SSR markers was constructed.Genetic analysis was conducted by mixed major gene plus polygene inheritance models,and quantitative trait loci (QTLs) identification by the QTLNetwork 2.0 and the composite interval mapping approach of WinQTLCart 2.5 software.Results showed that the PA trait was controlled by two major genes plus polygenes,mainly by major genes.Eight QTLs for PA were detected by the QTLNetwork 2.0 software,and each locus explained 0.01% to 39.89% of the phenotypic variation.Twelve QTLs for PA were detected by the WinQTLCart 2.5 software,with each locus explaining 2.83% to 30.60% of the phenotypic variation.Two major QTLs (qPA9.2 and qPA9.5) distributed between RM3700 and RM3600 and between RM5652 and RM410,respectively,and a moderate QTL (qPA9.7) distributed between RM257 and OSR28,were both detected by the two methods in all of the four environments.The negative effect alleles of the three QTLs were from Xiushui 79.In addition,eight pairs of epistatic QTLs with minor effects were also detected.QTL × environment interactions were not significant for additive QTLs and epistatic QTL pairs.     

利用基于条件表型值的关联分析发掘粳稻生育期和单株有效穗数有利等位变异

 发掘控制粳稻生育期和单株有效穗数的有利等位变异和携带有利等位变异的载体材料,为培育适应性广和产量竞争优势强的杂交粳稻组合提供遗传信息和育种材料。以94个粳稻品种构成的自然群体为试验材料,调查2个环境下各品种的生育期、单株有效穗数和株高,采用QGAStation软件中线性模型的方法进行条件表型值的转换,并利用TASSEL软件中的GLM进行生育期和单株有效穗数的基于非条件和条件表型值的关联分析。2个环境下共检测到34个与生育期和单株有效穗数相关联的SSR标记位点,其中15个与生育期关联,19个与单株有效穗数关联。RM8095 120 bp、RM7102 176 bp、RM72 170 bp和RM72 178 bp是与生育期关联的4个有利等位变异,其载体品种分别是红芒沙粳、日本晴、红芒沙粳和南农粳62401。将这些载体品种中的有利等位变异导入改良材料中,可缩短生育期2.03~9.93 d。RM72 182 bp是与单株有效穗数关联的有利等位变异,其载体材料为小青种。将小青种中的RM72 182 bp条带导入改良材料中可以增加单株有效穗数3个左右。且利用上述载体材料中的有利等位变异改良目标性状时不会对另外2个性状产生影响。     

国际稻种质资源农艺性状和稻瘟病抗性的初步评价

选用国际水稻遗传评价网(INGER)的稻种资源75份,分别在福州和上杭茶地种植,考察其主要农艺性状和苗期稻瘟病抗性表现。结果表明:大部分供试材料表现为生育期长、株型适中、分蘖力较强、谷粒细长;苗期稻瘟病抗性0~5级的有16份,其中,抗性好的有3份。综合农艺性状和稻瘟病抗性评价,初步筛选出8份优异资源,可供基础研究与育种利用。     

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.     

一个新的水稻半矮化小穗突变体的遗传分析与基因定位

 从粳稻中花 11转基因后代中发现了一个半矮化小穗突变体,表现为植株半矮化、生长势弱、半包茎穗、穗型变小等特点,将其命名为sd sp2(semi dwarf and small panicle 2)。遗传分析显示,该突变体表型受1对隐性核基因控制。以sd sp2突变体为母本与龙特甫B杂交构建F2分离群体,将该基因定位在水稻第6染色体的RH6 32和RH6 40之间的116 kb的物理距离内。通过水稻基因组注释系统在此区域预测到14个开放阅读框,未发现与已报道穗型发育相关基因的同源基因。     

Relationships of Panicle Type Index with Subspecies Characteristics and Yield Traits in Filial Generation of Crosses between Indica and Japonica Rice

Two recombinant inbred line(RIL)populations,one derived from a cross between Zhongyouzao 8(indica)and Toyonishiki(japonica)and the other from a cross between Qishanzhan(indica)and Akihikari(japonica),were grown in Liaoning and Sichuan Provinces,China,to study the panicle type index(PTI,the ratio of a number of node position on panicle axis where the secondary branch with the most numerous secondary branch grains is located to the number of primary branches)and its relationships with subspecies characteristi...     

Mining Elite Alleles of Growth Duration and Productive Panicle Number per Plant by Association Mapping with Conditional Phenotypic Value in Japonica Rice

To provide genetic information and materials for breeding hybrid japonica rice with wide adaptability and strong competitive advantage of yield,elite alleles and their carrier varieties of growth duration (GD) and productive panicle number per plant (PN) were detected.A natural population composed of 94 japonica varieties was phenotyped for the GD,PN and plant height (PH) in two environments.The conditional phenotypic data were transferred by the linear model method in software QGAStation 1.0,and association mapping based on the unconditional and conditional phenotype values of GD and PN was analyzed by using general linear model in software TASSEL.A total of 34 simple sequence repeat (SSR) marker loci associated with GD and PN were detected in the two environments.Among them,15 were associated with GD,and 19 were associated with PN.Four elite alleles of RM8095-120bp,RM7102-176bp,RM72-170bp and RM72-178bp were associated with GD,and their carrier varieties were Hongmangshajing,Nipponbare,Hongmangshajing and Nannongjing 62401,respectively.These elite alleles from the carrier varieties can shorten GD by 2.03 9.93 d when they were introduced into improved materials.RM72-182bp associated with PN was an elite allele,and its carrier variety was Xiaoqingzhong.It can increase PN by three when introduced into improved materials.Moreover,these elite alleles can be used to improve target traits without influencing another two traits.     

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.     

不同生态环境下水稻穗部性状QTL鉴定

【目的】发掘与产量相关的穗粒性状QTL对进一步克隆和利用高产基因具有重要意义。【方法】以超级粳稻龙稻5号和典型高产籼稻中优早8号杂交衍生的重组自交系群体为试材,在4种环境下对穗部性状进行比较和QTL分析。【结果】共检测到63个穗部性状QTL,分布于除第9染色体外的11条染色体上。在4个环境下分别检测到27、27、18和35个QTL。其中,16个QTL能在2个环境下被检测到,12个在3个以上环境下稳定表达,分别占QTL总数的25.40%和19.05%;第1、3、4和5染色体的多效QTL簇能在不同环境下稳定表达,对穗部性状具有明显的调控作用。【结论】第3染色体STS3.3-STS3.6区间的qSNP3、第4染色体RM5688-RM1359区间的qSNP4.1是2个新的稳定表达的多效性QTL簇。此外,上位性效应是调控穗部性状的重要组分。