Genetics of Soybean-Heterodera glycines Interactions

The soybean cyst nematode, Heterodera glycines, is one of the most economically important pathogens of soybean. Effective management of the nematode is often dependent on the planting of resistant soybean cultivars. During the past 40 years, more than 60 soybean genotypes and plant introductions (PI) have been reported as resistant to H. glycines. About 130 modern soybean cultivars registered in the United States are resistant to certain races of H. glycines. Several resistance genes have been identified and genetically mapped; however, resistance levels in many soybean cultivars are not durable. Some older cultivars are no longer resistant to certain H. glycines populations in many production areas, especially if a soybean monoculture has been practiced. Past soybean registration reports show that all resistant cultivars developed in public institutions from the mid-1960s to the present have been derived from five PIs. This narrow genetic background is fragile. To further complicate the issue, soybean-H. glycines genetic interactions are complex and poorly understood. Studies to identify soybean resistance genes sometimes have overlapped, and the same genes may have been reported several times and designated by different names. Nevertheless, many potential resistance genes in existing germplasm resources have not yet been characterized. Clearly, it is necessary to identify new resistance genes, develop more precise selection methods, and integrate these resistance genes into new cultivars. Rational deployment of resistant cultivars is critical to future sustained soybean production.     

Genetic Diversity of Soybean and the Establishment of a Core Collection Focused on Resistance to Soybean Cyst Nematode

Soybean cyst nematode （SCN; Heterodera glycines） Is one of the most Important pests affecting soybean production. The best method of control of SCN is through the development of resistant cultlvars. However, limited progress has been made in soybean breeding In China because most modern cultlvars have no resistance to SCN. The distribution and phenotype of 432 immune or highly resistant Chinese accessions were surveyed and a primary core collection was selected as a representative sample for further analyses. Using evenly distributed simple sequence repeat markers, five selection methods were applied to the primary core collection and the optimal method was chosen to establish a core collection, which consisted of 28 accessions. These encompassed 70.8% of the ailelic variation present in the overall resistant collection. The 28 accessions differed from the reference resistant accessions at the genomlc level, Indicating that Chinese resistant accessions are distinct from known resistant accessions. This applied core collection provides a rational framework for undertaking diversity surveys, using genetic variation for the investigation of complex traits and for the discovery of novel traits.     

东南亚稻种资源收集与鉴定评价

通过实地考察收集等途径,从东南亚国家引进稻种资源662份,其中野生稻120份,栽培稻542份。对栽培稻资源进行隔离检疫、繁殖以及性状鉴定,获得足够种子并构建引进东南亚栽培稻资源数据库。从栽培稻种质中鉴定发掘出抗褐飞虱材料58份,抗稻瘟病材料9份,抗白叶枯病材料11份,耐盐材料12份。引进的稻种资源拓宽了我国水稻遗传基础,丰富了我国的稻种资源基因库,将在水稻育种及相关研究中发挥积极的作用。     

Molecular characterization of apricot germplasm from an old stone collection

Increasing germplasm erosion requires the recovery and conservation of traditional cultivars before they disappear. Here we present a particular case in Spain where a thorough prospection of local fruit tree species was performed in the 1950s with detailed data of the origin of each genotype but, unfortunately, the accessions are no longer conserved in ex situ germplasm collections. However, for most of those cultivars, an old stone collection is still preserved. In order to analyze the diversity present at the time when the prospection was made and to which extent variability has been eroded, we developed a protocol in apricot (Prunus armeniaca L.) to obtain DNA from maternal tissues of the stones of a sufficient quality to be amplified by PCR. The results obtained have been compared with the results from the profiles developed from apricot cultivars currently conserved in ex situ germplasm collections. The results highlight the fact that most of the old accessions are not conserved ex situ but provide a tool to prioritize the recovery of particular cultivars. The approach used in this work can also be applied to other plant species where seeds have been preserved.     

国外大豆种质资源的基因挖掘利用现状与展望

中国已从美国和日本等22个国家引进大豆近等基因系、特殊遗传材料、大豆育成品种等2156份。经过评价已编入中国大豆品种资源目录。本文对国外引进大豆种质资源的特点及在中国研究与利用中所取得的成绩进行了总结,提出利用引进国外种质拓宽中国大豆品种遗传基础的表型和分子证据,回顾了国外种质在建立大豆抗胞囊线虫、抗疫霉根腐病、脂氧酶缺失、胰蛋白酶抑制剂缺失和抗草甘膦EPSP酶等特性的鉴定体系、标记和定位重要性状（耐盐性、抗大豆花叶病、无脂氧酶、无胰蛋白酶抑制剂）基因、开展分子标记辅助背景选择研究方面发挥的重要作用。我国大豆育种的实践证明,国外种质的利用促进了中国大豆新品种产量的增长、品质的改进和抗性的提高。因此,今后重视国外种质资源的有目的性的引进．加强时国外种质资源的深入研究,为国外种质资源在中国大豆遗传育种学、表型组学、基因组学、蛋白组学和酶学等领域的有效利用创造条件。     

Genetic divergence between North American ancestral soybean lines and introductions with resistance to soybean cyst nematode revealed by chloroplast haplotype

Domesticated soybean [Glycine max (L.) Merr.] is a major crop with an established ancestral relationship to wild soybean (Glycine soja Sieb. & Zucc.) native to Asia. Soybean genetic diversity can be assessed at different levels by identification of polymorphic alleles at genetic loci, in either the plastid or nuclear genomes. The objective of this study was to evaluate genetic diversity based on chloroplast haplotypes for soybean genotypes present in the USDA germplasm resource collection. Shared chloroplast haplotypes represent broad groups of genetic relatedness. Previous work categorized three-quarters of the cultivated soybeans from Asia into a single haplotype group. Our results confirmed the close relationship of North American soybean ancestors and G. max plant introductions previously identified as representing potential sources of soybean genetic variation with the finding that these genotypes belonged to a single chloroplast haplotype group. Genetic diversity was identified in soybean genotypes determined to have a high density of single nucleotide polymorphisms and in a screen of accessions with resistance to soybean cyst nematode. Characterization of soybean plant introduction lines into chloroplast haplotype group may be an important initial step in evaluating the appropriate use of particular soybean genotypes.     

Pan trapping soybean aphids (Hemiptera: Aphididae) using attractants

Since its introduction into the United States in the past 10 yr, soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), has been a damaging pest to soybean, Glycine max (L.) Merrill. During 2008 and 2009, fields in central and north central Iowa experienced pockets of high soybean aphid populations. Electroantennograms have shown that soybean aphid alatae are capable of detecting host plant volatiles and sex pheromones. Here, we evaluated baited pan traps as a potential soybean aphid attractant. Yellow pan traps were placed in soybean fields after planting along with lures that contained plant volatiles and sex pheromones in 2008 or sex pheromones only in 2009. Pan trap contents were collected weekly, and plant counts also were conducted. Aphids were identified, and soybean aphids were counted to determine whether one chemical lure was more attractive to spring migrants than other lures. In both years, soybean aphids collected in pan traps with lures were not significantly different from the other products tested.     

上海辰山植物园植物收集的现状和展望

上海辰山植物园于2005年开始筹建,与此同时启动了的植物收集工作。本文就辰山植物园基本情况、植物收集中长远规划、进展及技术策略进行了论述。活植物收集和标本收集是辰山植物园植物收集工作的两个方面。活植物收集包括以华东植物区系植物为主的物种收集和以上海适生的观赏植物为主的园艺品种收集,如鸢尾属、绣球属、荚蓬属、锦带属和绣线菊属的舭赏园艺品种。截止到2010年,辰山植物园共收集了9000种和园艺品种。其中,华东植物区系物种有1700种,来自世界范围专业苗圃的园艺品种有2800个,另有4500种和品种是种植于温室的热带和亚热带植物。目前共收集了近10000份标本,多数为研究和活植物收集的凭证标本,全部存放于上海辰山植物园标本馆（CSH）。     

上海辰山植物园植物收集的现状和展望

上海辰山植物园于2005年开始筹建,与此同时启动了的植物收集工作。本文就辰山植物园基本情况、植物收集中长远规划、进展及技术策略进行了论述。活植物收集和标本收集是辰山植物园植物收集工作的两个方面。活植物收集包括以华东植物区系植物为主的物种收集和以上海适生的观赏植物为主的园艺品种收集,如鸢尾属、绣球属、荚蒾属、锦带属和绣线菊属的观赏园艺品种。截止到2010年,辰山植物园共收集了9000种和园艺品种。其中,华东植物区系物种有1700种,来自世界范围专业苗圃的园艺品种有2800个,另有4500种和品种是种植于温室的热带和亚热带植物。目前共收集了近10000份标本,多数为研究和活植物收集的凭证标本,全部存放于上海辰山植物园标本馆（CSH）。     

国家基因库野生大豆（Glycine soja）资源最近十年考察与研究

总结了国家种质库最近10年野生大豆搜集进展和研究概况。我国野生大豆资源在1979-1982年间搜集并保存在国家基因库的为5939份;1996-2000年搜集了600份;2001-2010最近10年补充搜集了全国17个省(市、区)、318个县(市、旗)、930个乡镇(农场)。其中新搜集县市178个,共收集典型野生大豆资源1979份,野生大豆收集样品新增资源33.3%。     

Soybean germplasm pools in Asia revealed by nuclear SSRs

Soybean was domesticated in East Asia, where various kinds of landraces have been established as a result of adaptation to different environments and the diversification of food cultures. Asia is thus an important germplasm pool of soybean. In order to evaluate the genetic structure of the Asian soybean population, we analyzed allelic profiles at 20 simple-sequence repeat (SSR) loci of 131 accessions introduced from 14 Asian countries. The SSR loci produced an average of 11.9 alleles and a mean gene diversity of 0.782 in the accessions tested. Quantification theory III analysis and cluster analysis with the UPGMA method clearly separated the Japanese from the Chinese accessions, suggesting that the Japanese and Chinese populations formed different germplasm pools. The Korean accessions were involved in both germplasm pools, whereas most of the accessions from southeast and south/central Asia were derived from the Chinese pool. Relatively high genetic diversity and the absence of region-specific clusters in the southeast and south/central Asian populations suggest that soybean in these areas has been introduced repeatedly and independently from the diverse Chinese germplasm pool. The present study indicates that the two germplasm pools can be used as exotic genetic resources to enlarge the genetic bases of the respective Asian soybean populations.     

Two Erysiphe species associated with recent outbreak of soybean powdery mildew: results of molecular phylogenetic analysis based on nuclear rDNA sequences

 Serious outbreaks of powdery mildew by a fungus belonging to the mitosporic genus Oidium subgenus Pseudoidium have been reported on soybean (Glycine max) in a wide area of eastern Asia since 1998. The taxonomic and phylogenetic placement of the causal fungus has not yet been determined because of lack of the perfect stage. We found ascomata having mycelioid appendages on a single leaf of soybean infested by powdery mildew. Molecular phylogenetic analysis was conducted based on a total of 14 sequences of the rDNA internal transcribed spacer (ITS) region from 13 soybean and wild soybean (Glycine soja) materials collected in Japan, Korea, Vietnam, and the United States, combined with 47 sequence data obtained from the DNA databases. It was revealed that two Erysiphe species were associated with the outbreak of soybean powdery mildew. There was 16% difference between the two species in genetic divergence of the ITS sequence. One species with perfect stage has an ITS sequence identical to that of Erysiphe glycines on Amphicarpaea and is identified as Erysiphe glycines based on the ITS sequence and morphology of ascomata. The second species, without the perfect stage, is likely to be Erysiphe diffusa (= Microsphaera diffusa), known as the fungus causing soybean powdery mildew in the United States, because the ITS sequences are identical to those from materials collected in the United States. However, we need materials having ascomata of E. diffusa to confirm the species name. Received: March 15, 2002 / Accepted: May 22, 2002     

大豆基因组解析与重要农艺性状基因克隆研究进展

自2010年大豆(Glycine max)基因组论文在Nature杂志上正式发表以来, 以中国为主的多国科学家已对众多不同地理来源的野生大豆、农家品种及栽培品种进行了基因组重测序, 并通过比较基因组学等技术手段, 揭示了大豆基因组在进化与驯化过程中的基本规律。利用大豆基因组信息, 科学家已成功克隆了调控大豆生育期、生长(结荚)习性、种子形态性状与组分、结瘤与养分利用效率、生物及非生物胁迫抗(耐)性等重要农艺性状的功能基因, 并初步揭示了其相关的作用机理, 取得了一系列突破性进展, 为今后进一步精细解析大豆基因组与相关性状的基因调控网络奠定了坚实的基础, 同时为通过分子(模块)设计育种来培育新品种创造了必要条件。     

Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied.     

大豆微核心种质对草甘膦的耐受性鉴定

以萌发初期大豆弯曲的子叶节为靶点,利用草甘膦(Roundup)点施鉴定法,分析了221份大豆微核心种质的草甘膦耐受性及其与抗草甘膦转CP4-EPSPS基因大豆AG5601的差异,结果表明,草甘膦对不同大豆种质的抑制程度与点施的草甘膦浓度呈正相关,Roundup稀释浓度为1/1000、1/10000时,草甘膦对大豆生长几乎无影响;Roundup稀释浓度为1/10时,草甘膦显著抑制大豆生长,导致植株死亡;Roundup稀释浓度为1/100时,不同大豆种质对草甘膦耐受性差异显著,并鉴定出对草甘膦具有较好耐受性的种质10份。虽然大豆微核心种质对草甘膦的耐受程度远远低于AG5601,但不同大豆种质对草甘膦耐受性存在显著差异,这为利用转基因和杂交转育技术培育抗草甘膦转基因大豆的受体或轮回亲本的选择提供了理论依据。     

The southwestern origin and eastward dispersal of pear (<Emphasis Type="Italic">Pyrus pyrifolia</Emphasis>) in East Asia revealed by comprehensive genetic structure analysis with SSR markers

Pyrus pyrifolia is considered one of the most important cultivated Pyrus species. Hundreds of landraces and bred cultivars have been developed through the natural and artificial hybridizations necessary due to self-incompatibility. In this study, the genetic diversity of 478 Pyrus accessions, including Chinese landraces, bred cultivars, and wild samples, as well as introduced pear cultivars from Japan and Korea, was investigated with a set of 17 simple sequence repeat (SSR) markers distributed across all 17 linkage groups of the pear genome. A total of 121 alleles were detected, including 4 rare alleles with a frequency lower than 5%. Diversity statistics indicated a high level of genetic variation as quantified by the average values of the observed heterozygosity, the expected heterozygosity, and Wright’s fixation index, at 0.76, 0.78, and 0.02, respectively. Population structure and discriminant analysis of principal component analysis implied extensive genetic communication between sand pears in China and revealed four contiguous geographical clusters with overlapping geographical regions. The diversity of the four clusters and approximate Bayesian computation (ABC) indicated that sand pear spread from west to east along the Pearl River and Yangtze River valleys. High diversity and polyphyletic genetic components of cultivars in southwestern China further support southwestern China as the probable center of divergence for Pyrus species. A core collection of 80 out of 470 cultivars was selected, accounting for about 17% of accessions, and capturing 91% of all alleles, including all rare alleles. Our research provides a comprehensive understanding of sand pear germplasm in East Asia and constructs a preliminary core collection, which will be useful for association genetics studies, germplasm conservation, and breeding programs.     

The impact of cropland cover on river nutrient levels in the Mississippi River Basin

Aim This study developed high‐resolution datasets of the area of maize, soybean and wheat cultivation in the United States for 1950, 1970 and 1992. The datasets were used to examine the relationship between individual crop cover and nutrient levels in rivers across the Mississippi River Basin. Location This study was conducted in the United States, with focus on the Mississippi River Basin. Methods County and state‐level estimates of the planted area of maize, soybean and wheat were integrated with a satellite‐derived pattern in total cropland to develop 5′ × 5′ resolution datasets of the fractional area of maize, soybean and wheat in the United States for 1950, 1970 and 1992. Regression analysis was used to determine the relationships between mean levels of nitrogen, phosphorous and silica in 25 rivers across the Mississippi Basin, and the extent of maize, soybean and wheat cultivation in the watersheds. Results The crop datasets provide a spatially explicit representation of the area of the three primary crops in 1950, 1970 and 1992. The datasets clearly depict the rapid expansion of soybean cultivation, the increased specialization of individual agricultural regions, and the accompanying reduction in agricultural biodiversity since 1950. The statistical analysis identified strong correlations between the extent of maize and soybean cover in a watershed and the level of nitrogen (N) and phosphorous (P) at the watershed outlet. In particular, the area of maize appears to be strongly related to the concentration of total‐N and the ratio of dissolved inorganic‐N and organic‐N at the watershed outlet. Conclusions The intensification of cultivation of the three primary crops — maize, soybean and wheat — has altered land cover and water quality across the U.S. since 1950. The high present‐day rate of fertilizer use on maize and the expansion of soybean cultivation could be largely responsible for the change in nutrient ratios in the Mississippi River since 1950.     

Genetic diversity and population structure analysis of accessions in the US historic sweet sorghum collection

Sweet sorghum has the potential to become a versatile feedstock for large-scale bioenergy production given its sugar from stem juice, cellulose/hemicellulose from stalks, and starch from grain. However, for researchers to maximize its feedstock potential a first step includes additional evaluations of the 2,180 accessions with varied origins in the US historic sweet sorghum collection. To assess genetic diversity of this collection for bioenergy breeding and population structure for association mapping, we selected 96 accessions and genotyped them with 95 simple sequence repeat markers. Subsequent genetic diversity and population structure analysis methods identified four subpopulations in this panel, which correlated well with the geographic locations where these accessions originated or were collected. Model comparisons for three quantitative traits revealed different levels of population structure effects on flowering time, plant height, and brix. Our results suggest that diverse germplasm accessions curated from different geographical regions should be considered for plant breeding programs to develop sweet sorghum cultivars or hybrids, and that this sweet sorghum panel can be further explored for association mapping.