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.

Astrocytic calcium waves:unveiling their roles in sleep and arousal modulation

Neuron-astrocyte interactions are vital for the brain’s connectome.Understanding astrocyte activities is crucial for comprehending the complex neural network,particularly the population-level functions of neurons in different cortical states and associated behaviors in mammals.Studies on animal sleep and wakefulness have revealed distinct cortical synchrony patterns between neurons.Astrocytes,outnumbering neurons by nearly fivefold,support and regulate neuronal and synaptic function.Recent research on astrocyte activation during cortical state transitions has emphasized the influence of norepinephrine as a neurotransmitter and calcium waves as key components of ion channel signaling.This summary focuses on a few recent studies investigating astrocyte-neuron interactions in mouse models during sleep,wakefulness,and arousal levels,exploring the involvement of noradrenaline signaling,ion channels,and glutamatergic signaling in different cortical states.These findings highlight the significant impact of astrocytes on large-scale neuronal networks,influencing brain activity and responsiveness.Targeting astrocytic signaling pathways shows promise for treating sleep disorders and arousal dysregulation.More research is needed to understand astrocytic calcium signaling in different brain regions and its implications for dysregulated brain states,requiring future human studies to comprehensively investigate neuron-astrocyte interactions and pave the way for therapeutic interventions in sleep-and arousal-related disorders.

GSW3.1,a novel gene controlling grain size and weight in rice

Grain size and weight are closely related traits determining yield in rice(Oryza sativa L.).Since indica and japonica rice varieties differ significantly in multiple traits,a high-generation recombinant inbred line(RIL)population derived from the crossing LH9(indica)and RPY(japonica)was used to map grainrelated traits in six environments.Pyramiding of the quantitative trait loci(QTL)for thousand-grain weight showed that combinations of multiple QTL significantly increased the phenotypic effect.A novel gene named GSW3.1 controlling grain size and weight was discovered using the major QTL for the colocalization of grain width and thousand-grain weight on chromosome 3.Gene editing revealed that GSW3.1(LOC_Os03g16850)was pleiotropic,positively regulating grain size and weight while affecting several other agronomic traits.Haplotype analysis indicated that some traits,including grain width and weight,were highly correlated with indica-japonica differentiation.

Systematic functional interrogation of genome-wide association studies locus 17p13.3 deciphered role and genetic control of FAM57A in colorectal cancer development

Objective: Genome-wide association studies(GWAS) have identified over 150 risk loci linked to colorectal cancer(CRC), including the 17p13.3 locus with the tag single nucleotide polymorphism(SNP) rs12603526 in the Asian population. However, the specific causal gene and the functional regulatory mechanisms in this region remain unresolved, necessitating further investigation to elucidate the underlying mechanisms of CRC.Methods: We employed an RNA interference-based functional approach to identify genes critical for CRC cell proliferation at the GWAS locus 17p13.3. Bioinformatic fine-mapping analysis was conducted to prioritize causal variants. A large-scale study involving 7,013 cases and 7,329 controls from a Chinese population, along with another cohort of 5,158 cases and 20,632 controls from the UK Biobank, was performed to validate the association between the candidate variant and the gene. A series of biological experiments was conducted to explore the function of the candidate gene and its regulatory mechanisms.Results: We identified FAM57A as a key oncogene that promotes CRC cell proliferation, and confirmed its carcinogenic role through in vitro proliferation assays. The variant rs526835 was prioritized as a causal candidate for CRC risk, located in a functional region with enhancer properties, and showed a significant quantitative association with FAM57A expression. The rs526835 [T] variant was associated with a 1.17-fold increase in CRC risk [95%confidence interval(95% CI): 1.11-1.23, P=1.23×10^(−9)] in the large-scale Chinese cohort, which was further corroborated in the UK Biobank cohort. Mechanistically, we demonstrated that rs526835 enhances a promoterenhancer interaction mediated by the transcription factor JUN, leading to increased expression of FAM57A.Conclusions: We reveal the underlying mechanisms of CRC predisposition at the GWAS locus 17p13.3.Additionally, our findings highlight the critical role of FAM57A in CRC pathogenesis and introduce a novel enhancer-promoter interaction between FAM57A and rs526835, which could inform future precision prevention and personalized cancer therapies.

菜薹花芽分化及BrcuFLC基因的克隆与表达

通过制作石蜡切片研究了菜薹[Brassi cacampestris L.ssp.chinensis （L.） Makinovar.utilis Tsen et Lee]早熟品种‘油青四九’和晚熟品种‘油青甜菜心80天’的花芽分化过程，结果表明，当展开2-3片真叶时花芽分化开始启动。用已报道的拟南芥Flowering locus C（FLC）基因和FRIGIDA（FRI）基因的保守区域设计引物，通过RT-PCR的方法从两个菜薹品种中均克隆得到了两个决定开花的关键基因，并命名为BrcuFLC（GenBank登录号为EF138603）和BrcuFRI（GenBank登录号为EU700362）。半定量式RT-PCR表达分析表明，BrcuFLC基因在早、晚熟菜薹品种的不同发育时期表达存在差异，表达量随真叶数增加而逐步减少，但在晚熟品种中BrcuFLC表达量降低幅度小；BrcuFRI则在早、晚熟品种的所有阶段表达都较低。BrcuFLC在菜薹不同部位表达的情况不同，在茎、叶中的表达强，花次之，根中表达较弱；而Brcu-FRI在早、晚熟品种根中的表达量明显高于其它3个部位。

不同氮水平下玉米苗期生长性状及成熟期产量的QTL定位

【目的】研究玉米苗期氮素利用效率相关性状与成熟期产量之间的遗传关系。【方法】以优良杂交种豫玉22两亲本Z3和87-1为基础构建的一套F8家系的RIL群体为研究材料,在高、低氮两种条件下,通过苗期水培试验和成熟期田间试验,利用复合区间作图法对玉米苗期地上部干重、根干重、总根长、根冠比以及成熟期产量性状进行了QTL定位。【结果】利用Windows QTL Cartographer2.5软件,在LOD>2.5条件下共定位到22个QTL位点,其中高氮下定位到10个QTL,低氮下定位到12个QTL,两种氮水平下共位或紧密连锁的QTL位点很少,表明不同氮水平下的遗传机制不同。在第5和第7染色体上发现了苗期根系相关性状与成熟期产量之间存在连锁关系。【结论】苗期根系性状对成熟期的产量形成具有重要的作用,在氮高效遗传育种中可以把苗期根系性状作为一个重要的选择指标。

Comparative Microsatellite Analysis of Grass Carp Genomes of Two Gynogenetic Groups and the Xiangjiang River Group

The genomes of three groups of grass carp, namely the Xiangjiang River grass carp group （Xiangjiang group）, a one-generation artificially induced meio-gynogenetic grass carp group （meio-gynogenetic-1 group）, and a two-generation artificially induced meio-gynogenetic grass carp group （meio-gynogenetic-2 group）, were comparatively analyzed with microsatellite markers. Genetic polymorphism had been observed in the Xiangjiang group and most of the examined loci had more than two alleles. But the degree of genetic diversity was not very high. Although all the examined genetic loci in the analyzed individuals were in homozygous state, the genotypes of different individuals of the group were not identical in the meio-gynogenetic-1 group. In the meio-gynogenetic-2 group, not only the examined genetic loci of each individual were homozygous but also the genotypes of all the analyzed individuals of the group were the same. These results suggested that the examined meio-gynogenetic-2 group is a homozygous group and homozygous clone could be produced by continuous artificial induction of gynogenesis for two generations. It was found that the polymorphism existed not only at the allele level but also at the locus level; many alleles of the microsatellite loci and some of the microsatellite loci had been lost during the process of artificial gynogenesis. Therefore, both protection of the diversity of natural grass carp resource and selection of homozygous traits with desired economic genotypes are very important aspects for grass carp breeding.

大豆开花基因GmCO和GmFT的克隆及表达

为了研究大豆光周期反应是否受开花基因CO(CONSTANS)和FT(FLOWERING LOCUS T)调控,采用同源序列法从大豆中分离了CO和FT的同源物GmCO和GmFT.GmCO和GmFT分别编码151和109个氨基酸,与水稻和拟南芥中相关蛋白的氨基酸序列同源性达到70%以上.通过RT-PCR分析GmCO和GmFT在短日照(short daylength,SD)、自然光照(natural light,NL)和长日照(long daylength,LD)处理大豆不同发育阶段叶片中的表达发现,GmCO在LD处理大豆早期发育的叶片中高丰度表达,GmFT在SD和NL处理大豆开花时期的叶片中高丰度表达.上述结果表明,GmCO和GmFT的表达与大豆开花时间及光照长度密切相关,且GmCO抑制GmFT的表达.

玉米株高和穗位高遗传基础的QTL剖析

利用玉米强优势组合(Mo17×黄早四)自交衍生的191个F2单株构建了由SSR和AFLP标记组成的分子连锁图谱。F2进一步自交产生的184个F2∶3家系用于调查株高和穗位高的表型值。采用基于混合线性模型的复合区间作图法和相应的作图软件QTLmapper/V2.0,分别定位了7个株高和6个穗位高QTL;检测到18对控制株高和13对控制穗位高的上位性效应位点;同时发现了与环境存在显著互作的6个株高和8个穗位高单位点标记区域以及4对株高和4对穗位高上位性效应区域。分析了各种遗传因素在株高和穗位高遗传基础中的相对作用大小,指出了加性、显性和上位性是玉米株高和穗位高的重要遗传基础。并对所定位的QTL的真实性、株高和穗位高的关系以及研究结果对分子育种的启示予以讨论。

Genetic Diversity of Microsatellite DNA Loci of Tibetan Antelope(Chiru,Pantholops hodgsonii)in Hoh Xil National Nature Reserve,Qinghai,China

The Tibetan antelope （Pantholops hodgsonii）, indigenous to China, became an endangered species because of considerable reduction both in number and distribution during the 20th century. Presently, it is listed as an Appendix Ⅰ species by CITES and as Category I by the Key Protected Wildlife List of China. Understanding the genetic diversity and population structure of the Tibetan antelope is significant for the development of effective conservation plans that will ensure the recovery and future persistence of this species. Twenty-five microsatellites were selected to obtain loci with sufficient levels of polymorphism that can provide information for the analysis of population structure. Among the 25 loci that were examined, nine of them showed high levels of genetic diversity. The nine variable loci （MCM38, MNS64, IOBT395, MCMAL TGLA68, BM1329, BMSI341, BM3501, and MB066） were used to examine the genetic diversity of the Tibetan antelope （n = 75） in Hoh Xil National Nature Reserve（HXNNR）, Qinghai, China. The results obtained by estimating the number of population suggested that all the 75 Tibetan antelope samples were from the same population. The mean number of alleles per locus was 9.4 ± 0.5300 （range, 7-12） and the mean effective number of alleles was 6.519± 0.5271 （range, 4.676-9.169）. The observed mean and expected heterozygosity were 0.844 ± 0.0133 （range, 0.791-0.897） and 0.838 ± 0.0132 （range, 0.786-0.891）, respectively. Mean Polymorphism Information Content （PIC） was 0.818 ± 0.0158 （range, 0.753-0.881）. The value of Fixation index （Fis） ranged from -0.269 to -0.097 with the mean of -0.163 ± 0.0197. Mean Shannon＇s information index was 1.990 ± 0.0719 among nine loci （range, 1.660-2.315）. These results provide baseline data for the evaluation of the level of genetic variation in Tibetan antelope, which will be important for the development of conservation strategies in future.

利用RIL群体比较定位糙米和精米蛋白质含量的QTL

稻米蛋白质含量是水稻(Oryzasativa L.)营养品质育种的重要内容之一。本研究以珍汕97与南洋占杂交构建的重组自交系(RIL)群体为材料,结合其建立了由190个SSR标记组成的遗传图谱,利用QTLmap-per1.6对糙米和精米中的蛋白质含量的遗传基础进行了分析,共定位到4个控制糙米含量的QTLs和2个控制精米含量的QTLs。其中,控制精米蛋白质含量的2个QTLs与控制糙米蛋白质含量的2个QTLs位置一致,这2个QTL(qpc1和qpc2)在糙米和精米的蛋白质含量中均解释了较大的表型变异,而且糙米和精米蛋白质含量的相关系数为0.814,这表明糙米和精米的蛋白质含量具有相似的遗传基础。研究还发现上位性在糙米和精米蛋白质含量的遗传中也起很重要的作用。其中,在糙米蛋白质含量中,上位性QTLs可以解释42.2%的表型变异;在精米蛋白质含量中,上位性QTLs共解释了27.8%的表型变异。本研究初步揭示了稻米蛋白质含量的遗传基础,为分子标记辅助选择改良稻米品质及蛋白质含量基因的克隆提供了有益的信息。

山核桃FLOWERING LOCUS T同源基因的克隆与序列分析

根据不同植物FLOWERING LOCUST（FT）同源基因序列的保守区，设计合成1对长度为18bp的PCR简并引物，以山核桃基因组DNA为模板，采用PCR方法扩增出长度为152bp的DNA片段，克隆到pMD19-T载体上。测序及序列分析结果表明，扩增所获得的片段序列为FT基因第四外显子部分序列，不含内含子，推测共编码50个氨基酸；其序列在GenBank中注册号为FJ858260．1，同源性比对结果表明，其氨基酸序列与其他植物FT基因的同源性高达88％～96％。

橡胶树HbFCA启动子的克隆及其在橡胶树中的表达分析

FCA(Flowering control locus A)基因是自主开花调控途径中的关键调控基因之一,同时,FCA功能具有多样性。本研究中,利用TAIL-PCR方法获得2 039 bp橡胶树FCA基因的启动子序列,生物信息学分析发现该启动子中具有28种顺式调控元件,其中主要为基因表达调控核心元件(TAAT-box和CAAT-box)和光响应调控元件。此外,还含有激素、胁迫信号和光周期的顺式作用元件。同时,将橡胶树FCA启动子与GUS基因融合构建植物表达载体转化橡胶树,发现在胚状体、叶片和树根中GUS基因均强烈表达,但在茎段中表达较弱,说明橡胶树FCA基因除参与开花调控外,还可能参与多种发育过程的调控。本研究获得的HbFCA启动子转化橡胶树植株为进一步分析HbFCA基因功能及表达调控模式提供了遗传材料。

Influence of Epistasis and QTL×Environment Interaction on Heading Date of Rice(Oryza sativa L.)

QTLs for heading date of rice （Oryza sativa L.） with additive, epistatic, and QTL × environment （QE） interaction effects were studied using a mixed-model-based composite interval mapping （MCIM） method and a double haploid （DH） population derived from IR64/Azucena in two crop seasons. Fourteen QTLs conferring heading date in rice, which were distributed on ten chromosomes except for chromosomes 5 and 9, were detected. Among these QTLs, eight had single-locus effects, five pairs had double-locus interaction effects, and two single-loci and one pair of double-loci showed QTL × environment interaction effects. All predicted values of QTL effects varied from 1.179 days to 2.549 days, with corresponding contribution ratios of 1.04%-4.84%. On the basis of the effects of the QTLs, the total genetic effects on rice heading date for the two parents and the two superior lines were predicted, and the putative reasons for discrepancies between predicted values and observed values, and the genetic potentiality in the DH population for improvement of heading date were discussed. These results are in agreement with previous results for heading date in rice, and the results provide further information, which indicate that both epistasis and QE interaction are important genetic basis for determining heading date in rice.

QTL Analysis of Grain Storage Durability for Maize Under Controlled Deterioration Conditions Using SSR Markers

[Objective] This study aimed to analyze the quantitative trait loci （QTLs） of grain storage durability for maize under controlled deterioration conditions by using SSR markers. [Method] The recombinant inbred line population F 2 derived from the cross of shen 137/02-50 was used to do the simple sequence repeats （SSRs） and QTL analysis. [Result] The 2 parents showed good polymorphisms. Three loci were detected on chromosome 1, chromosome 6 and chromosome 9, accounting for 41.2% of total phenotypic. [Conclusion] This study provided theoretical basis for using molecular marker to assist the breeding of storage durable maize varieties.

Analysis on Quantitative Trait Loci for Resistance to Rice False Smut under Different Environmental Conditions

A recombinant inbred line （RILs） population with 157 lines derived from an inter-subspecies cross of Daguandao （japonica）/IR28 （indica） by the single seed de-scent method was used to detect quantitative trait loci （QTLs） conferring resistance to rice false smut caused by Ustilaginoidea virens（Cooke） Takahashi in Nanjing and Yangzhou. The disease rate index of the two parents and 157 RILs caused by rice false smut were scored and the QTLs for rice false smut resistance were detected accordingly by QTL Cartographer software. Eight QTLs control ing false smut resis-tance were detected on chromosomes 1, 2, 4, 8, 10, 11 and 12, respectively, with the phenotypic variance of 8.6%-22.5%. There were five QTLs detected in Nanjing and Yangzhou, respectively, and only two QTLs were found in both two years, the phenotypic variation was explained by individual QTL ranged from 18.0% to 18.9% for these two QTLs, and the additive effects of these two QTLs contributed to the 8.0%-14.6% decrease of disease index and therefore the disease resistance increased. The direction of the additive effects at six loci qFsr1, qFsr2, qFsr8, qFsr10a, qFsr11 and qFsr12 coincided with that predicted by phenotypes of the parents, and the IR28 al eles at these loci had positive effect against rice false smut while the negative effects were found in Daguandao al eles at qFsr4 and qFsr10b. Both qFsr10a and qFsr11 should be useful in rice breeding for resistance to rice false smut in marker-assisted selection （MAS） program.

抽薹开花抑制因子FLC表观遗传调控研究进展

FLOWERING LOCUS C(FLC)是植物抽薹开花调控网络中关键的开花决定因子。随着表观遗传学的发展,人们发现组蛋白修饰等表观调控FLC的表达在植物抽薹开花时间调控中起着非常重要的作用。FLC的抑制因子或促进因子通过改变组蛋白氨基酸的共价修饰(如乙酰化、甲基化等),影响FLC基因所在区域的染色质重塑,调控FLC转录表达水平,从而调节植物抽薹开花。本文就近年来国内外对植物抽薹开花关键调控基因FLC及表观遗传调控其表达研究现状进行了综述,并针对目前研究中存在的问题提出了今后的研究方向和重点。

Mapping QTLs for Panicle Traits Based on Rice RIL Population Derived from TD70 and Kasalath

Two hundred and forty recombinant inbred lines （RIL） derived from a cross TD70/Kasalath and its linkage map including 141 SSR markers were used to map QTLs controlling panicle length （PL）, total seeds per panicle （TSP） and grain density （GD） in 2010 and 2011. The results showed that a total of 23 QTLs controlling three panicle traits were detected on chromosomes 2, 3, 4, 6, 7, 8 and 10, respec- tively, including 5 QTLs controlling PL, 8 QTLs controlling TSP, 10 QTLs controlling GD, with the LOD value ranging between 2.5-9.3, and the QTLs explained the ob- served phenotypic by 4.0%-20.8%. The marker interval RM5699-RM424 on chro- mosome 2, RM489-RM1278 on chromosome 3, RM3367-RM1018 on chromosome 4, RM3343-RM412 on chromosome 6 were common marker intervals for TSP and GD; six QTLs （qPL3, qTSP4, qTSP6-2, qTSP7, qGD3-2 and qGDT） were detected in two years. Among these QTLs, the qPL3, qTSP6-2, qGD3-2 and qGD7 were major QTLs. All QTLs for PL mapped in the present study had been mapped QTLs previously by other research groups, 16 QTLs controlling TSP and GD were new ones which contributed the observed phenotypic variance range by 4%-9.5%. These results laid a founda^ion for further fine positioning or cloning these QTLs.

Microsatellite Variation Within Three Populations of Inbred C57BL/6J Strain

The goal of this study was to investigate the genetic stability of the C57BL/6J （B6） inbred mouse strain maintained in different breeders. Three populations of B6, Popl and Pop2 purchased from Beijing and Pop3 purchased from Shanghai, were examined. Fifteen microsatellite loci reported to be polymorphic among inbred strains were amplified using FAM labeled primers and genotyped with ABI Prism 377 automated sequencer. Seven loci were found polymorphic, and all the loci were homozygous in all the three populations. The present study indicates that genetic variation occurs in different B6 populations although they are still inbred in each breeder. The mechanism of genetic variation is not well understood now, but it is very important to know the precise content of the B6 genome before use of this strain in research.

用生存分析模型挖掘LY6E基因表达与胃癌放疗敏感性关系研究

目的:验证Lymphocyte antigen 6 complex,locus E (LY6E)的表达与胃癌放疗敏感性有联系的这一假设。方法:采用TCGA数据库中公开的胃癌数据,将胃癌的数据随机地分为两部分,一份作为测试数据,另一份作为验证数据。以P值为0. 05作为显著性判断标准。结果:LY6E的表达对于胃癌患者的总生存无明显联系;在测试和验证数据中,LY6E高表达的胃癌患者在放疗与非放疗两组间的总生存差异无统计学意义(P>0. 05),多因素调整后仍然无统计学意义(P> 0. 05)。多因素调整后,验证数据与测试数据的HR值分别为0. 72(0. 29-1. 76)和1. 28(0. 47-3. 47),P值为0. 47和0. 63;另一方面,在LY6E低表达的胃癌患者中,放疗组的生存率比非放疗组有着明显的提高,验证数据与测试数据的HR值调整后为0. 05(0. 005-0. 46)和0. 06(0. 01-0. 36),P值为8. 39*10-3和2. 36*10-3。结论:低表达的LY6E与胃癌放疗敏感性有明显的关联,LY6E低表达的患者接受放疗后生存率明显升高,表明LY6E是胃癌精准放疗的潜在的有效分子标记物。