Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton(Gossypium hirsutum L.)

Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and AvgD.Subsequently,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for AvgD.Among them,eight QTLs were repeatedly detected in two or more traits.Integrating these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the roots.Furthermore,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture formation.Collectively,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.

Genetic dissection and origin of pleiotropic loci underlying multilevel fiber quality traits in upland cotton(Gossypium hirsutum L.)

Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products.However,the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity,fineness,and neps,which in turn has impeded the genetic improvement and industrial utilization of cotton fiber.Here,12 single fiber quality traits were measured using Advanced Fiber Information System(AFIS)equipment among 383 accessions of upland cotton(Gossypium hirsutum L.).In addition,eight conventional fiber quality traits were assessed by the High Volume Instrument(HVI)System.Genome-wide association study(GWAS),linkage disequilibrium(LD)block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality traits.As a result,the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this study.More importantly,three novel pleiotropic loci(FM_A03,FF_A05,and FN_A07)regulating fiber maturity,fineness and neps,respectively,were detected based on AFIS traits.Numerous highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses,including the reported GhKRP6 for fiber length,the newly identified GhMAP8 for maturity and GhDFR for fineness.The origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11,FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton landraces.These findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in G.hirsutum.

Analyses and identifications of quantitative trait loci and candidate genes controlling mesocotyl elongation in rice

Rice direct seeding has the significant potential to save labor and water,conserve environmental resources,and reduce greenhouse gas emissions tremendously.Therefore,rice direct seeding is becoming the major cultivation technology applied to rice production in many countries.Identifying and utilizing genes controlling mesocotyl elongation is an effective approach to accelerate breeding procedures and meet the requirements for direct-seeded rice(DSR) production.This study used a permanent mapping population with 144 recombinant inbred lines(RILs) and 2 828 bin-markers to detect quantitative trait loci(QTLs) associated with mesocotyl length in 2019 and 2020.The mesocotyl lengths of the rice RILs and their parents,Lijiangxintuanheigu(LTH) and Shennong 265(SN265),were measured in a growth chamber at 30°C in a dark environment.A total of 16 QTLs for mesocotyl length were identified on chromosomes 1(2),2(4),3(2),4,5,6,7,9,11(2),and 12.Seven of these QTLs,including qML1a,qML1b,qML2d,qML3a,qML3b,qML5,and qML11b,were reproducibly detected in both years via the interval mapping method.The major QTL,qML3a,was reidentified in two years via the composite interval mapping method.A total of 10 to 413 annotated genes for each QTL were identified in their smallest genetic intervals of 37.69 kb to 2.78 Mb,respectively.Thirteen predicted genes within a relatively small genetic interval(88.18 kb) of the major mesocotyl elongation QTL,qML3a,were more thoroughly analyzed.Finally,the coding DNA sequence variations among SN265,LTH,and Nipponbare indicated that the LOC_Os03g50550 gene was the strongest candidate gene for the qML3a QTL controlling the mesocotyl elongation.This LOC_Os03g50550 gene encodes a mitogen-activated protein kinase.Relative gene expression analysis using qRT-RCR further revealed that the expression levels of the LOC_Os03g50550 gene in the mesocotyl of LTH were significantly lower than in the mesocotyl of SN265.In conclusion,these results further strengthen our knowledge about rice’s genetic mechanisms of mesocotyl elongation.This investigation’s discoveries will help to accelerate breeding programs for new DSR variety development.

Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach

Background:Aspergillus fumigatus(Af)is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic back-ground.The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus(Af)using an RNAseq approach in CC lines and hepatic gene expression.Methods:We studied 31 male mice from 25 CC lines at 8 weeks old;the mice were infected with Af.Liver tissues were extracted from these mice 5 days post-infection,and next-generation RNA-sequencing(RNAseq)was performed.The GENE-E analysis platform was used to generate a clustered heat map matrix.Results:Significant variation in body weight changes between CC lines was ob-served.Hepatic gene expression revealed 12 top prioritized candidate genes differ-entially expressed in resistant versus susceptible mice based on body weight changes.Interestingly,three candidate genes are located within genomic intervals of the previ-ously mapped quantitative trait loci(QTL),including Gm16270 and Stox1 on chromo-some 10 and Gm11033 on chromosome 8.Conclusions:Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af.As a next step,eQTL analysis will be performed for our RNA-Seq data.Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.

Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean

Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean. The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem. In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line(RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the Tstage, and the six-leaf stage as the flowering critical stage was designated as the Tstage. In total, 200 single nucleotide polymorphism(SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the Tstage, and 109 detected at the Tstage. Among these SNP loci, one SNP cluster(s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the Tstage, and the elite haplotype showed significantly greater plant height than the others. Meanwhile, one pleiotropic SNP cluster(ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the Tstage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition. Furthermore, four co-associated SNP loci(ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the Tand Tstages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population. More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels after low phosphorus treatment, and three of them were further verified by q RT-PCR. Thus, these genetic loci and candidate genes could be applied in markerassisted selection or map-based gene cloning for the genetic improvement of soybean phosphorus utilization.

Genome-wide association study reveals candidate genes for gummy stem blight resistance in cucumber

Gummy stem blight(GSB),caused by Didymella bryoniae,is a serious fungal disease that leads to decline in cucumber yield and quality.The molecular mechanism of GSB resistance in cucumber remains unclear.Here,we investigated the GSB resistance of cucumber core germplasms from four geographic groups at the seedling and adult stages.A total of 9 SNPs related to GSB resistance at the seedling stage and 26 SNPs at the adult stage were identified,of which some are co-localized to previously mapped Quantitative trait loci(QTLs)for GSB resistance(gsb3.2/gsb3.3,gsb5.1,and gsb-s6.2).Based on haplotype analysis and expression levels after inoculation,four candidate genes were identified within the region identified by both Genome-wide association study(GWAS)and previous identified QTL mapping,including Csa3G129470 for gsb3.2/gsb3.3,Csa5G606820 and Csa5G606850 for gsb5.1,and Csa6G079730 for gsb-s6.2.The novel GSB resistant accessions,significant SNPs,and candidate genes facilitate the breeding of GSB resistant cucumber cultivars and provide a novel idea for understanding GSB resistance mechanism in cucumber.

Mining candidate genes of grape berry cracking based on high density genetic map

Fruit cracking is a phenomenon in which the peel cracks during grape berry development,which seriously affects the yield and quality of the fruit.However,there are few studies on the mining of candidate genes related to berry cracking.In order to better understand the genetic basis of berry cracking,we used the results of previous quantitative trait locus(QTL)mapping,combined with field surveys of berry-cracking types and the berry-cracking rate,to mine candidate berry-cracking genes.The results showed that three identical QTL loci were detected in two years(2019 and 2020);and three candidate genes were annotated in the QTL interval.In mature berries,the expressions of the candidate genes were more abundant in the cracking-susceptible parent(‘Crimson Seedless’)than in the cracking-resistant parent(‘Muscat Hamburg’).Grape berry cracking is a complex trait controlled by multiple genes,mainly including genes encoding cellulose synthase–like protein H1,glucan endo-1,3-beta-glucosidase 12,and brassinosteroid insensitive 1-associated receptor kinase 1.The high expression of the candidate berry-cracking genes may promote the occurrence of berry cracking.This study helps elucidate the genetic mechanism of grape berry cracking.

Candidate genes for mastitis resistance in dairy cattle:a data integration approach

Background Inflammation of the mammary tissue(mastitis)is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector.Improving mastitis resistance is becoming an important goal in dairy ruminant breeding programmes.However,mastitis resistance is a complex trait and identification of mastitis-associated alleles in livestock is difficult.Currently,the only applicable approach to identify candidate loci for complex traits in large farm animals is to combine different information that supports the functionality of the identified genomic regions with respect to a complex trait.Methods To identify the most promising candidate loci for mastitis resistance we integrated heterogeneous data from multiple sources and compiled the information into a comprehensive database of mastitis-associated candidate loci.Mastitis-associated candidate genes reported in association,expression,and mouse model studies were collected by searching the relevant literature and databases.The collected data were integrated into a single database,screened for overlaps,and used for gene set enrichment analysis.Results The database contains candidate genes from association and expression studies and relevant transgenic mouse models.The 2448 collected candidate loci are evenly distributed across bovine chromosomes.Data integration and analysis revealed overlaps between different studies and/or with mastitis-associated QTL,revealing promising candidate genes for mastitis resistance.Conclusion Mastitis resistance is a complex trait influenced by numerous alleles.Based on the number of independent studies,we were able to prioritise candidate genes and propose a list of the 22 most promising.To our knowledge this is the most comprehensive database of mastitis associated candidate genes and could be helpful in selecting genes for functional validation studies.

ADAMTS-7基因rs3825807及rs1994016位点多态性与KD发病及CAL的关联性分析

目的分析ADAMTS-7基因rs3825807、rs1994016位点多态性与川崎病(KD)发病及其冠状动脉损伤(CAL)是否存在关联性。方法选取KD患儿100例为KD组,健康体检儿童100例为健康组。提取两组外周血DNA进行基因测序,比较两组ADAMTS-7基因rs3825807位点及rs1994016位点的多态性差异。KD组根据是否存在冠状动脉损伤分为冠状动脉损伤组(KD-CAL组)和无冠状动脉损伤组(KD-NCAL组),比较两组ADAMTS-7基因rs3825807位点及rs1994016位点的多态性差异。结果KD组与健康组比较,KD-NCAL组与KD-CAL组比较,ADAMTS-7基因rs3825807位点A、G等位基因频率和AA、AG、GG基因型频率以及rs1994016位点C、T等位基因频率和CC、CT、TT基因型频率差异均无统计学意义(P>0.05)。结论ADAMTS-7基因rs3825807、rs1994016位点多态性与KD的发病及CAL不存在明显关联性。

中华绒螯蟹MIH基因SNP位点筛选及其与生长性状的关联分析

为明确蜕皮抑制激素基因(MIH)对中华绒螯蟹的生长调控机制,本研究选取100只中华绒螯蟹幼蟹个体,分析幼蟹MIH基因的单核苷酸多态性(SNP)位点及基因型,并对与生长指标相关的多态性位点进行连锁不平衡和单倍型分析,进一步明确多态性位点单倍型与生长性状之间的相关性。结果显示,在中华绒螯蟹幼蟹MIH基因中共筛选鉴定出5个SNP位点,其中3个位点(C640G、C2529T和G2595T)与中华绒螯蟹生长性状具有相关性;3个相关位点中共检测到5种单倍型,其中H1单倍型(GCG)的占比最高(68.8%),为优势单倍型;H3单倍型(GTT)个体的生长性状指标最高,显著高于H2单倍型(CCG)。本研究得到的中华绒螯蟹MIH基因上3个与生长性状相关的SNP位点,可作为候选分子标记用于中华绒螯蟹优质品种选育。

基于全基因组关联分析的水稻穗长QTL定位及其候选基因分析

分别于2021年和2022年在湖南长沙种植254份水稻3K种质资源,在成熟期测定各种质的穗长。结合种质基因型进行全基因组关联分析,共检测到3个穗长QTL,分布于水稻第1、5、6号染色体,分别命名为qPL-1、qPL-5和qPL-6,相对贡献率为9.06%~28.27%;结合QTL区间内基因功能注释和基因不同单倍型的穗长差异显著性分析结果,最终获得qPL-1、qPL-5和qPL-6的候选基因,其中qPL-6与sped1-D共定位,Os01g0715600、Os05g0132700为调控穗长的新候选基因;对Os01g0715600、Os05g0132700和Os06g0597500的单倍型进行聚合分析,发现这3个基因存在累加效应。

柯乐猪XDH基因多态性鉴定及其对繁殖性状的影响

【目的】明确黄嘌呤脱氢酶基因(XDH)单核苷酸多态性(SNP)位点与柯乐猪繁殖性状的关联性,为加速柯乐猪的育种进程提供理论依据。【方法】选取87头健康经产柯乐母猪为研究对象,采用Sanger测序法筛查出XDH基因SNP位点,利用SPSS 22.0中的一般线性模型(GLM)分析SNP位点与柯乐猪繁殖性状指标(产活仔数、初生窝重、平均初生重、断奶仔猪数、断奶窝重及平均断奶重)的关联性,并通过RNAfold web server、ExPASy-ProtParam、NovoPro和SWISS-MODEL等在线软件进行生物信息学分析。【结果】在柯乐猪XDH基因上共筛选获得12个SNPs位点,分别是第33内含子上的g.108047658C>G和g.108047680C>A位点,第34内含子上的g.108048009C>T、g.108048044T>C、g.108048046T>C、g.108048047C>T、g.108048054C>T、g.108048153A>T、g.108048208A>G、g.108048212T>C和g.108048242C>T位点,第34外显子上的g.108047915G>A位点。12个SNPs位点均存在3种基因型,属于中度多态位点(0.25<PIC<0.50);g.108048047C>T、g.108048208A>G、g.108048242C>T、g.108048044T>C、g.108048046T>C和g.108048212T>C位点的基因型分布符合Hardy-Weinberg平衡状态(PHWE>0.05),其余6个SNPs位点的基因型分布则显著偏离Hardy-Weinberg平衡状态(PHWE<0.05)。除g.108047658C>G位点与g.108047680C>A位点、g.108048044T>C位点与g.108048046T>C位点、g.108048046T>C位点与g.108048047C>T位点间存在强连锁不平衡关系外,其余各SNP位点间均不存在强连锁不平衡关系。g.108047658C>G和g.108047915G>A位点对柯乐猪产活仔数的影响达显著水平(P<0.05,下同),g.108047658C>G位点表现为CG基因型个体的产活仔数显著高于GG基因型个体,g.108047915G>A位点表现为AG基因型个体的产活仔数显著高于AA基因型个体。g.108047915G>A位点突变导致柯乐猪XDH基因mRNA二级结构发生改变,最小自由能由-1508.90 kcal/mol上升到-1507.80 kcal/mol;且XDH基因等位基因G的突变还导致其编码蛋白分子式、相对分子量、理论等电点(pI)、不稳定系数及蛋白高级结构发生改变。【结论】柯乐猪XDH基因第33内含子g.108047658C>G位点和第34外显子g.108047915G>A位点对其产活仔数的影响达显著水平,可作为柯乐猪繁殖性状改良的潜在分子辅助标记。

玉米双胚遗传机制研究进展

高产一直是玉米育种的研究热点,传统方式提高玉米产量已进入瓶颈期,玉米双胚这种特殊遗传现象可能为获得高产提供突破性方向。为了解双胚现象发生的遗传机制,本文归纳了包括玉米等多种作物双胚、多胚现象的前人研究,从多维度整合了相关的遗传表现、细胞学观察、生理生化特性、分子机制研究等内容。此外,本文总结了有关双胚的部分研究方法,为双胚性状的分子遗传机制及玉米高产育种研究提供可行性参考。通过前人研究,本文发现玉米双胚基因挖掘方面暂未有突破性进展,因此预测有关双胚现象的研究重点仍是影响双胚性状表达的关键遗传位点的定位与候选基因的挖掘,以进一步解析玉米双胚现象的分子网络机制,为指导玉米高产育种提供理论支撑。

Assessment of molecular markers and marker-assisted selection for drought tolerance in barley(Hordeum vulgare L.)

This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in barley.The accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome cv.Morex.Six common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAS to improve the grain yield and yield components in barley under drought stress.These strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAS in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.

服用硝苯地平原发性高血压患者的药物基因组学研究

目的基于药物基因组学技术,分析服用硝苯地平原发性高血压患者药物相关基因多态性分布情况,评估基因导向使用硝苯地平的应用价值。方法选取2021年10月至2023年10月收治的485例服用硝苯地平的原发性高血压患者作为研究对象,分析硝苯地平药物相关基因,并进一步分析各基因多态性位点基因型分布情况,比较不同疗效、有无下肢水肿患者各基因多态性位点基因型分布情况,行单因素、多因素Logistic回归分析基因多态性位点与疗效、下肢水肿的关系。结果细胞色素P450(CYP)3A5*3 A6986、尿素转运型糖蛋白A2抗体(SLC14A2)rs1123617、SLC14A2 rs3745009、CYP3A4 rs2242480、肾上腺素能α_(1)A受体(ADRA1A)rs1048101、肾上腺素能β1受体(ADRB1)c.1165、肾上腺素能β2受体(ADRB2)rs1042713、血管紧张素转换酶(ACE)rs4646994基因多态性均符合Hardy-Weinberg平衡定律,说明样本具有代表性。不同疗效、有无下肢水肿患者CYP3A5*3 A6986、CYP3A4 rs2242480、ADRB1 c.1165、ADRB2 rs1042713、ACE rs4646994位点基因型比较,差异有统计学意义(P<0.05,P<0.01);而SLC14A2 rs1123617、SLC14A2 rs3745009、ADRA1A rs1048101位点基因型比较无统计学差异(P>0.05)。单因素、多因素Logistic回归分析显示,CYP3A5*3 A6986 G>A、CYP3A4 rs2242480 C>T、ADRB1 c.1165 C>G、ADRB2 rs1042713 G>A、ACE rs4646994 I>D与服用硝苯地平原发性高血压患者疗效、下肢水肿显著相关(P<0.01)。结论服用硝苯地平原发性高血压患者药物相关基因多态性与疗效、下肢水肿密切相关,可为临床医师制订个性化治疗方案提供参考。

长顺绿壳蛋鸡GRIN1基因3′非翻译区的多态性及其与蛋壳品质的关联性

【目的】探索长顺绿壳蛋鸡GRIN1基因3′非翻译区(untranslated region,UTR)多态性对蛋壳品质的影响。【方法】选择185只健康蛋鸡,测定其第45周龄产蛋的蛋质量、蛋形指数、蛋壳强度、蛋壳厚度和蛋壳质量5个指标;使用NCBI和PrimerPremier 3.0设计引物,采用正向测序法筛选GRIN1基因在3′UTR区域的SNP位点。【结果】GRIN1基因的3′UTR检测到4个SNP位点:g.30871C>T、g.31017A>G、g.31158A>C和g.31166G>C,其中仅g.31158A>C和g.31166G>C之间存在强连锁不平衡,且g.30871C>T和g.31017A>G都极显著偏离哈代—温伯格平衡(P<0.01)。g.31017A>G与蛋壳品质的关联分析中,GG基因型的蛋质量显著高于AA基因型(P<0.05)。4个SNP位点共产生5个单倍型(H1、H2、H3、H4、H5)和8个双倍型(H1H1、H1H2、H1H3、H2H2、H2H3、H2H4、H3H5、H4H4),双倍型H3H5的蛋质量显著高于双倍型H2H2和H2H3(P<0.05),双倍型H3H5的蛋壳质量显著高于双倍型H2H2(P<0.05),其他双倍型指标间的差异未达到显著水平(P>0.05)。【结论】长顺绿壳蛋鸡GRIN1基因与蛋壳品质存在显著关联;g.31017A>G对蛋壳品质有显著影响,能够作为改善蛋壳品质的分子标记位点参考。

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.

Introduction of rol Genes into Cotton (Gossypium hirsutum L.) Genome and Effects of Transgene Expression on the Plant Development

The rol genes cloned from Agrobacterium rhizogenes were transferred to the cotton genomevia Agrobacterium-mediated transformation. Molecular analyses and developmentalidentification of the putative transgenic plants were carried out by means of PCR,Southern blotting and field characterization. The results showed that the expression ofrol genes greatly increased the rooting ability of the transgenic plants, and changed theplant development. Highly male-sterile plants with strong apical dominance and fertileplants with short internodes, stunted growth and improved economic characteristics weresegregated from the T1 transgenic lines of wild rol B gene and the rol B gene driven by35S promoter. The transgenic lines of rol ABC construct usually had normal boll settingand slow growth. Therefore we concluded that the rol genes, modified in suitable ways,could be used to create new cotton varieties with some highly valuable characteristics.

Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319 on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175 annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23 pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

Genetic dissection of rice appearance quality and cooked rice elongation by genome-wide association study

Appearance and cooked rice elongation are key quality traits of rice. Although some QTL for these traits have been identified, understanding of the genetic relationship between them remains limited. In the present study, large phenotypic variation was observed in 760 accessions from the 3 K Rice Genomes Project for both appearance quality and cooked rice elongation. Most component traits of appearance quality and cooked rice elongation showed significant pairwise correlations, but a low correlation was found between appearance quality and cooked rice elongation. A genome-wide association study identified 74 QTL distributed on all 12 chromosomes for grain length, grain width, length to width ratio, degree of endosperm with chalkiness, rice elongation difference, and elongation index. Thirteen regions containing QTL stably expressed in multiple environments and/or exerting pleiotropic effects on multiple traits were detected. By gene-based association analysis and haplotype analysis, 46 candidate genes, including five cloned genes, and 49 favorable alleles were identified for these 13 QTL. The effect of the candidate gene Wx on rice elongation difference was validated by a transgenic strategy. These results shed light on the genetic bases of appearance quality and cooked rice elongation and provide gene resources for improving rice quality by molecular breeding.