Distribution and Selective Effects of Vrn-A1, Vrn-B1, and Vrn-D1 Genes in Derivative Varieties from Four Cornerstone Breeding Parents of Wheat in China

Vernalization, the process of a long exposure to low temperature to induce flowering in plants, is essential for plants to adapt to cold winters. The presence of vernalization genes Vrn-A1, -B1, and -D1 in four cornerstone breeding parents of wheat in China （Funo, Mentana, Yanda 1817, and Bima 4） and 322 derivative varieties （mostly winter wheat） from these parents were determined using PCR based molecular method. The frequencies of the VRN-1 genes in these derivative varieties were in order of Vrn-Dl（67.1%）〉 Vrn-Bl（19.6%）〉 Vrn-Al（5.3%）, which are similar as the former conclusion that Vrn-D1 is associated with the latest heading time, Vrn-A1 the earliest, and Vrn-B1 intermediate values. The frequencies of Vrn-Al and Vrn-B1 loci in the derivative varieties from winter wheat zones were higher than that from spring winter zones. Based on the wheat breeding history in China and the fact of non-random distribution of Vrn-A1 and Vrn-B1 in the derivative varieties from the four parents, there could be a strong selective effect on VRN-1 genes in different regions where the derivative varieties were cultivated.     

Progress on Mapping of Quantitative Trait Loci in Crops

Most important agricultural traits of crops are controlled by many genes. These traits have complicated genetic basis and are difficult for genetic analysis. Due to application of molecular marker techniques in the last two decades, genetic and molecular dissection of quantitative traits has become possible. In this paper, recent progress on mapping of quantitative trait loci in crops was reviewed.     

Advanced Backcross QTL Analysis for the Whole Plant Growth Duration Salt Tolerance in Rice（Oryza sativa L.）

Salinity is a major factor limiting rice yield in coastal areas of Asia. To facilitate breeding salt tolerant rice varieties, the wholeplant growth duration salt tolerance（ST） was genetically dissected by phenotyping two sets of BC2F5 introgression lines（ILs） for four yield traits under severe natural salt stress and non-stress filed conditions using SSR markers and the methods of advanced backcross QTL（AB-QTL） analysis and selective introgression. Many QTLs affecting four yield traits under salt stress and nonstress conditions were identified, most（〉90%） of which were clustered in 13 genomic regions of the rice genome and involved in complex epistasis. Most QTLs affecting yield traits were differentially expressed under salt stress and non-stress conditions. Our results suggested that genetics complementarily provides an adequate explanation for the hidden genetic diversity for ST observed in both IL populations. Some promising Huanghuazhan（HHZ） ILs with favorable donor alleles at multiple QTLs and significantly improved yield traits under salt stress and non-stress conditions were identified, providing excellent materials and relevant genetic information for improving rice ST by marker-assisted selection（MAS） or genome selection.     

Progress Towards Genetics and Breeding for Minor Genes Based Resistance to Ug99 and Other Rusts in CIMMYT High-Yielding Spring Wheat

Wheat rusts continue to cause significant losses worldwide despite major efforts given to their genetic control. This is due to frequent evolution and selection of virulence in pathogen overcoming the deployed race-specific resistance genes. Although the life of effective race-specific resistance genes can be prolonged by using gene combinations, an alternative approach being implemented at CIMMYT is to deploy varieties that posses adult plant resistance （APR） based on combinations of minor, slow rusting genes. When present alone, the APR genes do not confer adequate resistance especially under high disease pressure; however, combinations of 4 or 5 minor genes usually result in ＂near-immunity＂ or a high level of resistance. Although only a few APR genes are catalogued, various APR QTLs are now known and could lead to further characterization of additional genes. Four characterized genes have pleiotropic effects in conferring partial APR to all 3 rusts and powdery mildew, thus simplifying the task of breeding wheat varieties that are resistant to multiple diseases. Significant progress was made recently in developing high-yielding wheat germplasm that possesses high levels of APR to all three rusts by implementing a Mexico- Kenya shuttle breeding scheme. Parents with APR to Ug99 were hybridized with high-yielding parents that had adequate to high levels of APR to leaf rust and yellow rust. Segregating populations and advanced lines from these crosses were selected under high rust pressures in Mexico （leaf rust and yellow rust） and Kenya （Ug99 stem rust and yellow rust） to identify high- yielding progenies that possess high to adequate APR to all three rusts. International distribution of these high-yielding wheats is underway through CIMMYT intemational yield trials and screening nurseries. It is expected that several wheat varieties with APR to three rusts will be released and grown in various countries in the near-future that will allow determining the durability of resistance.     

Analysis on Genetic Similarity of Japonica Rice Variety from Different Origins of Geography in the World

The genetic similarity and genetic difference among improved japonica rice varieties from different countries （or regions and organizations） were detected. The aim is to provide genetic basis to the breeding of japonica rice varieties. The genetic similarity and cluster of 313 improved japonica varieties from 20 countries （or regions and organizations） were analyzed using the SSR marker. With 34 SSR primers which were polymorphic and uniformly distributed in rice genome, totally 198 alleles were detected among these improved varieties with the average number of alleles per pair of primers of 5.8235. RM320, RM531, RM1, RM21, and RM336 located more alleles, which were 16, 13, 12, 10, and 10 respectively. RM320, RM336, RM286, RM531, and RM21 showed higher genetic diversity indexes, which were 2.3668, 2.0041, 1.9684, 1.9508, and 1.7203, respectively. The genetic similarity for improved japonica varieties among different countries （or regions and organizations） were ranged from 0.279 to 0.918, and the mean value was 0.653. The rice varieties from countries whose latitude and geography position were all nearer were clustered together with higher genetic similarity indexes. The rice varieties from countries who had more different latitude and far geography position were clustered separately with lower genetic similarity indexes. The results indicated the genetic similarity indexes among improved japonica varieties had a close relationship with the geographical position, especially with the latitude.     

The Source of Genes Related to Rice Grain Starch Synthesis Among Cultivated Varieties and Its Contribution to Quality

The property of starch in rice grain endosperm is a very important determinant for rice quality, and it is essential to understand the genetic effect of the genes related to starch synthesis in high-yielding rice varieties for rice quality improvement. The physicochemical properties （e.g., amylose content, gel consistency, and RVA profile） were assessed on 53 rice varieties, including certain typical indica/japonica landraces and certain high-yielding modern varieties. And molecular markers for Sbel, Sbe3 developed on the basis of sequence diversities between the rice subspecies indica and japonica, together with PCR-Acc I marker for Wx gene were used to investigate the genotypes of 53 rice cultivars. The result showed that the developed molecular markers for Wx, Sbel, Sbe3 could distinguish indica or japonica alleles at three loci. Among all the 53 rice cultivars, six genotypes were observed when Sbel, Sbe3, and Wx loci were considered together, while the genotypes of WxiSbelJSbe3i and WxiSbelJSbe3J were absent. In order to explore the genetic effects of the three genes, especially for starch branching enzyme genes, ANOVA and multiple comparison analysis were conducted. The results showed that rice cultivars with different genotypes exhibited different phenotypes, including amylose content, gel consistency and certain RVA characteristics, and the significant differences among the six genotypes were observed. It was concluded that these three genes had randomly recombined during the process of the rice variety development. And the genetic effects of indica and japonica alleles at three gene loci were different, of which, Wx gene plays a major role in determining the starch properties, followed by Sbel and Sbe3, and the genetic effects of Sbel and Sbe3 in different backgrounds （Wx~, WxJ） are different. The results have provided a clue for rice good quality variety development, and the molecular markers will benefit to the improvement in quality of rice.     

Development of Genome-Wide Scan for Selection Signature in Farm Animals

Identifying targets of positive selection in farm animals has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of selection. This review described important recent results derived from the application of genome-wide scan to the study of genetic changes in farm animals. These included findings of regions of the genome that showed breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the implications for domestication. To date, sixteen genome-wide scans for recent or ongoing positive selection have been performed in farm animals. A key challenge is to begin synthesizing these newly constructed maps of selection into a coherent narrative of animal breed evolutionary history and derive a deeper mechanistic understanding of how animal populations improve or evolve. The major insights from the surveyed studies are highlighted and directions for future study are suggested.     

Allelic Variation in Loci for Adaptive Response and Its Effect on Agronomical Traits in Chinese Wheat （Triticum aestivum L.）

Heading date was an important trait that decided the adaptation of wheat to environments. It was modiifed by genes involved in vernalization response, photoperiod response and development rate. In this study, four loci Xgwm261, Xgwm219, Xbarc23 and Ppd-D1 which were previously reported related to heading time were analyzed based on three groups of wheat including landraces （L）, varieties bred before 1983 （B82） and after 1983 （A83） collected from Chinese wheat growing areas. Generally, heading date of landrace was longer than that of varieties. Signiifcant differences in the heading time existed within the groups, which implied that diversiifcation selection was much helpful for adaptation in each wheat zone. Photoperiod insensitive allele Ppd-D1a was the ifrst choice for both landrace and modern varieties, which promoted the heading date about four days earlier than that of sensitive allele Ppd-D1b. The three SSR loci had different characters in the three groups. Predominant allele combination for each zone was predicted for wheat group L and A83, which made great contribution to advantageous traits. Xgwm219 was found to be signiifcantly associated with heading date in Yellow and Huai River Winter Wheat Zone （Zone II） and spike length in Middle and lower Yangtze Valley Winter Wheat Zone （Zone III）, which implied functional diversiifcation for adaption. Variation for earliness genes provided here will be helpful for whet breeding in future climatic change.     

Construction of Genetic Linkage Map Based on SSR Markers in Peanut （Arachis hypogaea L.）

Molecular genetic maps of crop species can be used in a variety of ways in breeding and genomic research such as identification and mapping of genes and quantitative trait loci （QTLs） for morphological, physiological and economic traits of crop species. However, a comprehensive genetic linkage map for cultivated peanut has not yet been developed due to the extremely low frequency of DNA polymorphism in cultivated peanut. In this study, 142 recombinant inbred lines （RILs） derived from a cross between Yueyou 13 and Zhenzhuhei were used as mapping population in peanut （Arachis hypogaea L.）. A total 652 pairs of genomic-SSR primer and 392 pairs of EST-SSR primer were used to detect the polymorphisms between the two parents. 141 SSR primer pairs, 127 genomic-SSR and 14 EST-SSR ones, which can be used to detect polymorphisms between the two parents, were selected to analyze the RILs population. Thus, a linkage genetic map which consists of 131 SSR loci in 20 linkage groups, with a coverage of 679 cM and an average of 6.12 cM of inter-maker distance was constructed. The putative functions of 12 EST-SSR markers located on the map were analyzed. Eleven showed homology to gene sequences deposited in GenBank. This is the first report of construction of a comprehensive genetic map with SSR markers in peanut （Arachis hypogaea L.）. The map presented here will provide a genetic framework for mapping the qualitative and quantitative trait in peanut.     

选择牵连效应分析：发掘重要基因的新思路

作物在长期进化过程中，除自然选择外，还经历了两次大的人工选择，即人工驯化选择和育种选择，使栽培种与野生种之间、现代品种与古老的地方品种之间在群体遗传结构及性状上形成了很大的差异；在基因组中，一些承受强选择作用的基因在群体中的多样性显著降低，同时这些基因附近区域的遗传多样性也明显下降。在遗传学中将这种对个别基因的选择导致其侧翼区域遗传多样性降低的现象称之为选择牵连效应（Hitchhiking effect，也称选择搭载效应）。通过大群体多位点的扫描分析，可找到一些发生选择牵连效应的基因组区段，利用标记/性状关联分析（Marker/Trait association analysis），就可发现这些区段所控制的重要性状；对这些区段进行精细扫描和分析，即可找到一些决定重要农艺性状的基因，并发现优异等位变异，从而为重要基因的克隆和作物品种的分子设计奠定基础。各大作物高密度分子标记连锁图谱的绘制完成、高通量基因型分析技术体系的建立，为利用选择牵连效应分析、通过标记/性状之间的关联，寻找和定位一些重要基因奠定了基础。本文在查阅文献的基础上，结合作者的研究，以小麦株高、千粒重、磷的吸收和利用等性状为例，就选择牵连效应分析的基本思路、方法进行了讨论，以起到抛砖引玉之作用。     

新疆和西藏棕鳟群体的遗传多样性分析

【目的】了解新疆和西藏地区棕鳟养殖群体的遗传多样性状况,解析两地棕鳟的亲缘关系和遗传差异,为棕鳟的分子辅助育种打下数据和方法基础。【方法】采用第二代高通量测序技术对来自新疆达坂城和西藏亚东的2个棕鳟群体各12个个体进行基因组重测序,利用鉴定得到的多态性信息位点进行群体结构、群体遗传多样性和群体间的选择消除分析。【结果】...     

欧洲与东亚小麦品种遗传多样性的比较分析

 【目的】在分子水平上回答欧洲和东亚小麦品种的遗传关系和多样性差异；同时对Genomic-SSR（gSSR）和EST-SSR（eSSR）多态性水平进行比较分析。【方法】利用38个Genomic-SSR引物对和44对EST-SSR引物对分析371份欧洲小麦品种和363份东亚品种。【结果】共检测到865个等位变异，每个引物对的等位变异数为1～50，平均为10.42；多态性信息含量（PIC）为0～0.91, 平均为 0.53；欧洲和东亚品种分别检测到730、716个等位变异，特有等位变异分别为150、135，平均遗传丰富度分别为8.80和8.61，遗传多样性指数分别为 0.46 和0.52。欧洲和东亚小麦品种在聚类图上明显地划分为两大类群；每个国家或大区聚类结果与其地理分布基本一致，即相邻国家或地区的品种亲缘关系更近一些。近一半基因座的等位变异频率及其分布在欧洲与东亚材料间存在明显差异。 通过标记/性状关联分析，在4B、5A、6A、7B染色体上发现6个影响穗粒数、千粒重、株高、抽穗期、有效分蘖等重要农艺性状的基因座，其中个别基因座优势等位变异差异可能与东亚、欧洲品种的分化密切相关。中国20世纪50～80年代育成品种在大的聚类上明显靠近欧洲材料、而远离中国50年代以前的育成品种和地方品种，这与中国的育种实际相吻合。基于Genomic-SSR和基于EST-SSR的聚类图整体趋势是一致的，但由前者估算的遗传距离远高于后者，因此，一般的SSR较功能基因SSR更易发生变异，由育种选择所引起的分化更快。【结论】在中国今后的小麦育种中，需要通过杂交、回交，对欧洲品种的一些重要基因座等位变异（基因）进行置换，方有可能实现“洋为中用”的目的。     

Genetic study and molecular breeding for high phosphorus use efficiency in maize

Phosphorus is the second most important macronutrient after nitrogen and it has many vital functions in the life of plants. Most soils have a low available P content, which has become a key limiting factor for increasing crop production. Also, low P use efficiency (PUE) of crops in conjunction with excessive application of P fertilizers has resulted in serious environmental problems. Thus, dissecting the genetic architecture of crop PUE, mining related quantitative trait loci (QTL) and using molecular breeding methods to improve high PUE germplasm are of great significance and serve as an efficient approach for the development of sustainable agriculture. In this review, molecular and phenotypic characteristics of maize inbred lines with high PUE, related QTL and genes as well as low-P responses are summarized. Based on this, a breeding strategy applying genomic selection as the core, and integrating the existing genetic information and molecular breeding techniques is proposed for breeding high PUE maize inbred lines and hybrids.     

马铃薯品种（系）田间晚疫病抗性评价和全基因组遗传多样性分析

【目的】进行田间晚疫病抗性评价,利用SNP分子标记分析马铃薯抗晚疫病种质的遗传多样性及分离基因组内可能影响马铃薯晚疫病抗病性状的遗传区段,为马铃薯晚疫病抗性种质创新与利用提供理论依据。【方法】通过多年多点田间鉴定对马铃薯种质资源进行晚疫病抗性评价。利用dd-RAD技术对马铃薯种质资源进行简化基因组测序并分型SNP标记。利用Admixture软件分析群体的遗传结构,GCTA软件进行主成分分析,fastTree软件构建系统发育树,stacks程序包中的populations命令计算群体遗传多样性参数,vcftools程序计算选择性消除参数,Clustal Omega程序比对氨基酸序列,MEGA6绘制氨基酸序列进化树,GEMMA 0.98.1软件进行全基因组关联分析,CMplot程序绘制QQ图和曼哈顿图。【结果】通过对马铃薯种质资源多年多点田间晚疫病抗性进行鉴定,得到101个抗晚疫病的品种（系）及21个感病品种,并对它们进行dd-RAD简化基因组测序,通过对比参考基因组,共检测到分布相对均匀的8 697 602个SNP。通过种群结构分析、主成分分析和系统进化分析,将这些种质资源进一步划分为6个群体。6个群体之内的平均核苷酸多样性值（π）为0.2055—0.2572,之间的群体分化指数（Fst）为0.156909—0.187336,说明这些种质资源存在较丰富的单核苷酸多态性。同时6个群体内期望杂合度（He）为0.187—0.2297,观测杂合度（Ho）为0.0829—0.1186,6个群体内的观测杂合度均小于期望杂合度,并且6个群体内的近交系数（Fis）范围为0.2412—0.3554,说明在选育这些种质的过程中存在近交现象。分析可能影响晚疫病抗性的马铃薯基因组遗传区段,以20 kb为窗口,5 kb为步长,在基因组相同位置,分别计算不同抗性种质间π值比值和Fst值,进行选择性消除分析,选择π值比值最小的5%及Fst值最大的10%的745个遗传区段进行分析,遗传区段中共包含507个基因,其中,有4个NBS-LRR类基因。利用群体SNP和马铃薯种质的不同晚疫病抗性表型,进行全基因组关联分析,有9个SNP与抗病性状高度相关,其周围50 kb的基因组范围内,有69个基因,其中15个基因预测参与到应激反应,12个基因预测参与清除过氧化物自由基过程。【结论】dd-RAD简化基因组测序可以在马铃薯基因组中分型获得数量较多、分布相对均匀的SNP标记。马铃薯田间抗晚疫病种质资源拥有较丰富的单核苷酸多态性,但在其选育过程中存在近交现象。选择性清除和关联分析有助于分离影响晚疫病抗病性状的遗传区段。     

Genome-wide detection of selective signatures in a Duroc pig population

The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide. Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome. In this study, a Duroc pig population (n=715) was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler (GGP) Porcine Chip. The relative extended haplotype homozygosity (REHH) method was used for selective signature detection in a subset of the population (n=368), selected to represent a balanced family structure. In total, 154 significant core regions were detected as selective signatures (P<0.01), some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness. Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGF1. These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes. This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs.     

稻米品质的遗传研究及分子育种进展

水稻是我国最主要的粮食作物之一,高产优质不仅是水稻基础研究的重点,更是水稻育种应用的主要方向.稻米品质主要包含加工碾磨品质、外观品质、蒸煮食味品质和营养品质,是受遗传与环境因素共同影响的复杂性状.本文对稻米品质性状的分类、影响因素、遗传研究进展和稻米品质育种改良现状进行了综述,并对稻米品质研究进行总结和展望,以期为稻米...     

陆地棉吐絮率的限制性两阶段多位点全基因组关联分析及候选基因预测

[目的]吐絮率是反映陆地棉(Gossypium hirsutum L.)早熟性状的重要指标之一,利用全基因组关联分析(genome-wide association study,GWAS)解析吐絮率的QTL(quantitative trait locus)及其遗传效应,为陆地棉早熟性状的分子育种提供理论基础.[方法]...     

2020-11期目录

随着新一代基因组测序技术的快速发展，基因组选择技术在促进优良基因型精准高效选育方面展现了前所未有的应用前景。近年来，基因组选择在动植物数量性状遗传育种领域的研究进展引起了广泛关注，关于其在林木改良驯化中的应用 也逐渐被报道。本文通过综述基因组选择的基本概况、主要模型方法及其在动植物中的研究进展，进一步探讨了基因组选择在林木育种研究中的现状和发展趋势，强调了对预测模型优化与机器学习等新兴技术的引入与方法创新，提出了联合利用全基因组关联分析与基因组编辑技术的优化育种方案，为加快林木优良品种的精准选育提供了新思路。