玉米抗病虫性的分子标记研究进展

本文评述了近十年来利用分子标记研究玉米抗病虫性的进展。主要论述了抗病虫性基因定位中出现的问题、通过分子标记研究这些基因在基因组中的分布和基因组结构等,提出了玉米抗病虫性基因的标记和定位的发展方向和策略。     

Optimising the identification of causal variants across varying genetic architectures in crops

Association studies use statistical links between genetic markers and the phenotype variation across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome‐wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures. In this study, we employ real‐world genotype datasets from four crop species with distinct minor allele frequency distributions, population structures and linkage disequilibrium patterns. We demonstrate that different GWAS statistical approaches provide favourable trade‐offs between power and accuracy for traits controlled by different types of genetic architectures. FarmCPU provides the most favourable outcomes for moderately complex traits while a Bayesian approach adopted from genomic prediction provides the most favourable outcomes for extremely complex traits. We assert that by estimating the complexity of genetic architectures for target traits and selecting an appropriate statistical approach for the degree of complexity detected, researchers can substantially improve the ability to dissect the genetic factors controlling complex traits such as flowering time, plant height and yield component.     

An analysis of effects of heterozygosity in dairy cattle for bovine tuberculosis resistance

Genetic selection of cattle more resistant to bovine tuberculosis (bTB) may offer a complementary control strategy. Hypothesising underlying non‐additive genetic variation, we present an approach using genome‐wide high density markers to identify genomic loci with dominance effects on bTB resistance and to test previously published regions with heterozygote advantage in bTB. Our data comprised 1151 Holstein–Friesian cows from Northern Ireland, confirmed bTB cases and controls, genotyped with the 700K Illumina BeadChip. Genome‐wide markers were tested for associations between heterozygosity and bTB status using marker‐based relationships. Results were tested for robustness against genetic structure, and the genotypic frequencies of a significant locus were tested for departures from Hardy‐Weinberg equilibrium. Genomic regions identified in our study and in previous publications were tested for dominance effects. Genotypic effects were estimated through ASReml mixed models. A SNP (rs43032684) on chromosome 6 was significant at the chromosome‐wide level, explaining 1.7% of the phenotypic variance. In the controls, there were fewer heterozygotes for rs43032684 (P < 0.01) with the genotypic values suggesting that heterozygosity confers a heterozygote disadvantage. The region surrounding rs43032684 had a significant dominance effect (P < 0.01). SNP rs43032684 resides within a pseudogene with a parental gene involved in macrophage response to infection and within a copy‐number‐variation region previously associated with nematode resistance. No dominance effect was found for the region on chromosome 11, as indicated by a previous candidate region bTB study. These findings require further validation with large‐scale data.     

Beyond pathways: genetic dissection of tocopherol content in maize kernels by combining linkage and association analyses

Although tocopherols play an important role in plants and animals, the genetic architecture of tocopherol content in maize kernels has remained largely unknown. In this study, linkage and association analyses were conducted to examine the genetic architecture of tocopherol content in maize kernels. Forty‐one unique quantitative trait loci (QTLs) were identified by linkage mapping in six populations of recombinant inbred lines (RILs). In addition, 32 significant loci were detected via genome‐wide association study (GWAS), 18 of which colocalized with the QTLs identified by linkage mapping. Fine mapping of a major QTL validated the accuracy of GWAS and QTL mapping results and suggested a role for nontocopherol pathway genes in the modulation of natural tocopherol variation. We provided genome‐wide evidence that genes involved in fatty acid metabolism, chlorophyll metabolism and chloroplast function may affect natural variation in tocopherols. These findings were confirmed through mutant analysis of a particular gene from the fatty acid pathway. In addition, the favourable alleles for many of the significant SNPs/QTLs represented rare alleles in natural populations. Together, our results revealed many novel genes that are potentially involved in the variation of tocopherol content in maize kernels. Pyramiding of the favourable alleles of the newly elucidated genes and the well‐known tocopherol pathway genes would greatly improve tocopherol content in maize.     

外引玉米种质对两种穗腐病原镰孢菌抗性鉴定

采用双牙签接种技术,2016-2017年连续2年对从美国、加拿大、罗马尼亚、德国、法国、荷兰等国家引进的177份玉米种质资源抗玉米穗腐病原拟轮枝镰孢(F.verticillioides)和禾谷镰孢(F.graminearum)进行了鉴定。结果表明,鉴定的177份玉米种质资源中,对拟轮枝镰孢表现高抗(HR)的资源2份,占总数的1.13%;抗病(R)38份,占总数的21.47%;中抗(MR)75份,占总数的42.37%;感病(S)48份,占总数的27.12%;高感(HS)14份,占总数的7.91%。177份玉米种质资源中,对禾谷镰孢(F.graminearum)表现抗病(R)12份,占鉴定资源总数的6.78%;中抗(MR)66份,占总数的37.29%;感病(S)64份,占总数的36.16%;高感(HS)35份,占总数的19.77%,未发现对禾谷镰孢菌表现高抗的材料。在177份玉米种质资源中,兼抗两种穗腐病原镰孢菌的种质资源有12份。     

基因组时代林木抗病分子机理研究的新进展

林木的分子病理学研究长期以来落后于农业作物病理学。随着高通量测序技术的问世,林木的分子病理学研究迎来了一个崭新的时代。从2006年至今,杨树、云杉等重要森林树种的全基因组测序相继完成,这为全面解析林木的抗病过程提供了遗传背景。同时,转录组学和全基因组关联分析的应用使得人们能快速地积累大量的数据,从而为揭示林木和病原菌之间的分子互作机制奠定了基础。近两年来CRISPR/Cas9基因编辑等分子生物学技术创新不断。高效的分子生物学技术结合基因组学研究有利于林木育种的研究。以下阐述了林木对抗病原菌入侵的生理机制,综合论述了近十年来基因组学和转录组学研究在木本植物分子病理学方面所取得的成果,总结了分子生物学技术在林木抗病领域的研究成果,分析了存在的问题和未来发展的趋势,以期为林木抗病育种提供参考。     

单核苷酸多态性与甜瓜抗枯萎病分子育种研究

目的:结合单核苷酸多态性标记技术,利用甜瓜本身的抗病性以解决新疆甜瓜病害问题。方法:对新疆甜瓜抗枯萎病基因Fom-2基因进行克隆分析,并根据Fom-2基因在不同抗性甜瓜亲本的单核苷酸多态性,设计检测SNP标记的PCR扩增引物,验证其多态性;并利用F2代分析该标记与筛选获得的甜瓜抗枯萎病基因连锁的SSR标记的遗传关系。结果:在抗病与感病甜瓜品种中均扩增获得PCR条带,试验中设计单核苷酸多态性分子标记在抗病品种为显性,与筛选的和抗枯萎病基因紧密连锁的共显性标记SSR430共分离。结论:不同抗性甜瓜品种均含有Fom-2基因或其高度同源序列,SNP显性标记和共显性标记SSR430均可用于甜瓜抗枯萎病分子标记辅助育种。     

Metabolic GWAS‐based dissection of genetic bases underlying the diversity of plant metabolism

Plants have served as sources providing humans with metabolites for food and nutrition, biomaterials for living, and treatment for pain and disease. Plants produce a huge array of metabolites, with an immense diversity at both the population and individual levels. Dissection of the genetic bases for metabolic diversity has attracted increasing research attention. The concept of genome‐wide association study (GWAS) was extended to studies on the diversity of plant metabolome that benefitted from the development of mass‐spectrometry‐based analytical systems and genome sequencing technologies. Metabolic genome‐wide association study (mGWAS) is one of the most powerful tools for global identification of genetic determinants for diversity of plant metabolism. Recently, mGWAS has been performed for various species with continuous improvements, providing deeper insights into the genetic bases of metabolic diversity. In this review, we discuss fully the achievements to date and remaining challenges that are associated with both mGWAS and mGWAS‐based multi‐dimensional analysis. We begin with a summary of GWAS and its development based on statistical methods and populations. As variation in targeted traits is essential for GWAS, we review metabolic diversity and its rise at both the population and individual levels. Subsequently, the application of mGWAS for plants and its corresponding achievements are fully discussed. We address the current knowledge on mGWAS‐based multi‐dimensional analysis and emerging insights into the diversity of metabolism.     

Confirmation and fine‐mapping of clinical mastitis and somatic cell score QTL in Nordic Holstein cattle

A genome‐wide association study of 2098 progeny‐tested Nordic Holstein bulls genotyped for 36 387 SNPs on 29 autosomes was conducted to confirm and fine‐map quantitative trait loci (QTL) for mastitis traits identified earlier using linkage analysis with sparse microsatellite markers in the same population. We used linear mixed model analysis where a polygenic genetic effect was fitted as a random effect and single SNPs were successively included as fixed effects in the model. We detected 143 SNP‐by‐trait significant associations (P < 0.0001) on 20 chromosomes affecting mastitis‐related traits. Among them, 21 SNP‐by‐trait combinations exceeded the genome‐wide significant threshold. For 12 chromosomes, both the present association study and the previous linkage study detected QTL, and of these, six were in the same chromosomal locations. Strong associations of SNPs with mastitis traits were observed on bovine autosomes 6, 13, 14 and 20. Possible candidate genes for these QTL were identified. Identification of SNPs in linkage disequilibrium with QTL will enable marker‐based selection for mastitis resistance. The candidate genes identified should be further studied to detect candidate polymorphisms underlying these QTL.     

Genome of ‘Charleston Gray’, the principal American watermelon cultivar,and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.     

Mapping the four‐horned locus and testing the polled locus in three Chinese sheep breeds

Four‐horned sheep are an ideal animal model for illuminating the genetic basis of horn development. The objective of this study was to locate the genetic region responsible for the four‐horned phenotype and to verify a previously reported polled locus in three Chinese breeds. A genome‐wide association study (GWAS) was performed using 34 two‐horned and 32 four‐horned sheep from three Chinese indigenous breeds: Altay, Mongolian and Sishui Fur sheep. The top two significant single nucleotide polymorphisms (SNPs) associated with the four‐horned phenotype were both located in a region spanning positions 132.6 to 132.7 Mb on sheep chromosome 2. Similar locations for the four‐horned trait were previously identified in Jacob, Navajo‐Churro, Damara and Sishui Fur sheep, suggesting a common genetic component underlying the four‐horned phenotype. The two identified SNPs were both downstream of the metaxin 2 (MTX2) gene and the HOXD gene cluster. For the top SNP—OAR2:g.132619300G>A—the strong associations of the AA and AG genotypes with the four‐horned phenotype and the GG genotype with the two‐horned phenotype indicated the dominant inheritance of the four‐horned trait. No significant SNPs for the polled phenotype were identified in the GWAS analysis, and a PCR analysis for the detection of the 1.8‐kb insertion associated with polled sheep in other breeds failed to verify the association with polledness in the three Chinese breeds. This study supports the hypothesis that two different loci are responsible for horn existence and number. This study contributes to the understanding of the molecular regulation of horn development and enriches the knowledge of qualitative traits in domestic animals.     

Quantitative Genetics in the Genomics Era

The genetic analysis of quantitative or complex traits has been based mainly on statistical quantities such as genetic variances and heritability. These analyses continue to be developed, for example in studies of natural populations. Genomic methods are having an impact on progress and prospects. Actual relationships of individuals can be estimated enabling novel quantitative analyses. Increasing precision of linkage mapping is feasible with dense marker panels and designed stocks allowing multiple generations of recombination, and large SNP panels enable the use of genome wide association analysis utilising historical recombination. Whilst such analyses are identifying many loci for disease genes and traits such as height, typically each individually contributes a small amount of the variation. Only by fitting all SNPs without regard to significance can a high proportion be accounted for, so a classical polygenic model with near infinitesimally small effects remains a useful one. Theory indicates that a high proportion of variants will have low minor allele frequency, making detection difficult. Genomic selection, based on simultaneously fitting very dense markers and incorporating these with phenotypic data in breeding value prediction is revolutionising breeding programmes in agriculture and has a major potential role in human disease prediction.     

不同来源大麦对条纹病抗性鉴定及遗传多样性分析

为了解不同来源大麦对条纹病的抗性及遗传多样性,本研究采用"三明治法"通过人工接种大麦条纹病菌对91份大麦材料进行抗性评价,并通过31对SSR标记对91份大麦材料进行遗传多样性和群体结构分析。结果表明,人工接种大麦条纹病菌后共鉴定出4份免疫、6份高抗、33份抗病、43份感病和5份高感大麦材料;31对SSR标记共检测出等位基因238个,平均每对标记可检测到7.677个等位基因,等位基因数的变幅为2～19;主基因频率变化范围为0.236～0.951,平均值为0.394;基因多样性指数的变幅为0.094～0.871,平均值为0.667;多态性信息含量变幅为0.091～0.860,平均值为0.613;遗传相似系数变异范围为0.103～1.000,平均值为0.522;在遗传相似系数为0.783水平上可将参试材料聚为3个大类群,各大类分别包含86份、2份和3份材料;群体遗传结构分析表明,供试大麦材料分为3个亚群,每个亚群分别包含47份、33份和11份材料,且在91份材料中,Q>0.6的材料占总数的97.80%。本研究经抗病鉴定及分子标记结果综合分析,可为挑选抗病亲本辅助抗大麦条纹病优良品种的选...     

玉米抗南方锈病种质资源初步鉴定及遗传多样性分析

南方锈病是玉米生产上的重要病害。2013-2015年在广西南宁和北京昌平对903份玉米种质资源进行了抗南方锈病的初步鉴定与评价,并利用SSR标记对筛选出的部分抗性材料进行了遗传多样性分析。结果表明,在903份种质中,8份自交系在广西南宁和北京昌平均对南方锈病表现高抗(HR),占总鉴定种质的0.9%;29份材料表现为抗病(R),占比3.2%,包括27份自交系和2份农家种;中抗种质(MR)100份,占比11.1%;感病(S)和高感(HS)种质分别为181和585份,占鉴定材料的20.0%和64.8%。由此可见,玉米资源中高抗南方锈病的种质较为匮乏,在不同地点均表现高抗的材料是难得的抗源。不同地理来源的玉米种质对南方锈病的抗性水平存在较大差异,其中抗性资源较为丰富的是源自内蒙古和山西的种质。42对多态性SSR引物在50份抗锈病材料中,共扩增出141个条带,多态性条带139个,多态位点百分率(PPB)为98.58%。平均等位基因数(Na)1.98,平均有效等位基因数(Ne)1.59,平均Nei's基因多样性(H)0.34,平均多态性信息含量(PIC)0.78,平均Shannon's信息指数(I)0.51;通过UPGMA聚类分析,50份抗病材料被划分为2个类群,其中,第Ⅰ类群又可划分为5个亚类,表现出较高的遗传多样性,为抗病育种中抗源的选择和利用提供参考信息。     

The brown coat colour of Coppernecked goats is associated with a non‐synonymous variant at the TYRP1 locus on chromosome 8

The recent development of a goat SNP genotyping microarray enables genome‐wide association studies in this important livestock species. We investigated the genetic basis of the black and brown coat colour in Valais Blacknecked and Coppernecked goats. A genome‐wide association analysis using goat SNP50 BeadChip genotypes of 22 cases and 23 controls allowed us to map the locus for the brown coat colour to goat chromosome 8. The TYRP1 gene is located within the associated chromosomal region, and TYRP1 variants cause similar coat colour phenotypes in different species. We thus considered TYRP1 as a strong positional and functional candidate. We resequenced the caprine TYRP1 gene by Sanger and Illumina sequencing and identified two non‐synonymous variants, p.Ile478Thr and p.Gly496Asp, that might have a functional impact on the TYRP1 protein. However, based on the obtained pedigree and genotype data, the brown coat colour in these goats is not due to a single recessive loss‐of‐function allele. Surprisingly, the genotype distribution and the pedigree data suggest that the ⁴⁹⁶Asp allele might possibly act in a dominant manner. The ⁴⁹⁶Asp allele was present in 77 of 81 investigated Coppernecked goats and did not occur in black goats. This strongly suggests heterogeneity underlying the brown coat colour in Coppernecked goats. Functional experiments or targeted matings will be required to verify the unexpected preliminary findings.     

Detection and Molecular Diversity of Pantoea ananatis Associated with White Spot Disease in Maize,Sorghum and Crabgrass in Brazil

Bacteria of the genus Pantoea have become important plant pathogens worldwide in recent years. Pantoea ananatis was reported as the cause of maize white spot, a serious maize disease in Brazil, causing significant yield losses. However, very little information is available about how to detect this pathogen, its genetic variability and the putative alternative hosts in maize‐growing areas. To address these issues, we implemented a rapid and efficient PCR‐based method to identify P. ananatis isolated from leaves showing white spot symptoms and evaluated its genetic diversity in maize, sorghum and crabgrass. Of the 29 bacteria isolated from typical water‐soaked lesions of white spot disease that produced yellow colonies, 15 isolates were identified as P. ananatis by 16S rDNA sequencing and correctly detected by the PCR reaction, amplifying a specific fragment of the ice nucleation gene (ina). These P. ananatis isolates included 13 from maize, one from sorghum and one from crabgrass, while the other 14 yellow colony isolates were from other bacterial species, including two Pantoea species (Pantoea dispersa and Pantoea agglomerans) that were not amplified by the ina primers. These results indicate that the optimized PCR assay can be used to detect P. ananatis isolated from white spot lesions and could be used as a large‐scale and cost‐effective method of detecting this pathogen in leaf lesions on maize and other grasses. All isolates were evaluated for hypersensitive response (HR) on tobacco, revealing that some P. ananatis were able to induce HR. The high genetic variability revealed by rep‐PCR did not differentiated the P. ananatis isolates based on their hosts or HR reaction. The detection, characterization and diversity of P. ananatis from maize, sorghum and crabgrass in our study can be applied in understanding epidemiology and designing control strategies for maize white spot disease in Brazil.     

陕棉抗病种质及其衍生品种的遗传多样性与群体结构研究

通过72个分布于棉花全基因组的SSR标记,对54份陕棉抗病种质及其衍生品种的遗传多样性与群体结构进行了分析。结果表明:(1)54份陕棉种质间的遗传相似系数在0.733 3~0.987 2之间,其中材料间相似系数≤0.90的占11.1%,相似系数≥0.95的占55.6%,相似系数在0.90~0.95的占33.3%。(2)72个SSR标记等位基因变异的多态性信息含量(PIC值)在0.04~0.68,平均为0.33。(3)基于遗传距离的UPGMA聚类分析显示,在遗传相似系数为0.877时将54个品种分为5类,第Ⅰ类44个品种,第Ⅲ类7个品种,第Ⅱ、Ⅳ、Ⅴ类各1个品种。(4)基于数学模型的聚类和群体结构分析显示,54份种质归属于4个组群。研究认为,54份材料间遗传相似系数较大,遗传基础比较狭窄,多样性很低。