Stability of growth periods traits for soybean cultivars across multiple locations

The growth periods(GPs, from planting/emergence to reproductive stage 8(R8) of soybean cultivars vary in different ecological regions, especially in China with a very complex soybean cropping system. In this study, a 3-yr experimental study was undertaken in three geographical locations of China from 2008 to 2010, including the Northeast(40.66–45.85°N), Huang-Huai(34.75–38.04°N) and southern(22.82–30.60°N) eco-regions with about 250 accessions in each region to clarify the classification of maturity group(MG) and identify the cultivars with stable GP to increase the knowledge about the GP distribution of soybean cultivars in China. GPs of soybean cultivars in different eco-regions were significant different with a gradual decrease from 115–125 d in the Northeast part to the 85–100 d in the southern part of China. The geographical location was the major factor for GP of cultivars from the Northeast, while the year of planting was the major factor affecting the stability of GPs in Huang-Huai summer and southern summer soybean. AMMI2(additive main effects and multiplicativeinteraction)-Biplot analysis showed that the GPs of soybean cultivars from the Northeast eco-region have a comparatively satisfactory environmental stability. Moreover, soybean cultivars with moderate GP/MG and stable environment adaptability in different eco-regions were identified based on the linear regression and AMMI analysis, which was important for the accurate classification of soybean MGs in future. Taken together, our results reflected the genetic diversity, geographical distribution and environmental stability of the Chinese soybean GP trait. Soybean cultivars with stable GP for various Chinese eco-regions would be beneficial for Chinese soybean genetic improvement, varietal introduction, exchange, and soybean breeding program for wide adaptability.     

Analysis of Genetic Diversity in Natural Populations of huashanica Keng Using Microsatellite （SSR） Markers

Psathyrostachys huashanica Keng is endemic to China and only distributed in Huashan Mountain in Shaanxi Province, China. In this study, 15 P. huashanica populations consisting of 450 individuals sampled across their main distribution were investigated by using the simple sequence repeats （SSRs） markers. A total of 184 alleles were detected on 24 SSR loci, and the number of alleles on each locus ranged from 2 to15, with an average of 7.667. The total gene diversity （HT= 0.683） and the coefficient of population differentiation （GST = 0.125） showed that P. huashanica had a relatively high level of genetic variation, and the genetic variation was mainly distributed within the populations. The gene flow among the populations of P. huashanica （Nm = 1.750） was much less than that of the common anemophytes （Nm = 5.24）. Correlation analysis demonstrated that the number of alleles as well as genetic diversity of the five populations of Huangpu valley decreased along with the increase of altitudes, but the correlation was not significant. Implications of these results for future P. huashanica collection, evaluation and conservation were discussed.     

Analysis of SSRs Uncovers Hierarchical Structure and Genetic Diversity in Chinese Soybean Landraces

For clarifying the hierarchical patterns of population structure of soybean landraces in China, the seven clusters previously identified using Bayesian clustering of 1 504 soybean landraces based on SSR markers genotyping data were further analyzed. Using the largest value of AK, these landraces could be split into 20 sub-clusters, which was supported by highly significant pairwise Fst-values and generally in accordance with the geographic origin and sowing types. The autumn-sowing types ended up in one distinct sub-cluster from the otherwise summer-sowing type, where the autumn- sowing types are most likely derived from. The division into 20 sub-clusters explained 7.3% of the genetic variation, next to 9.7% present among the seven clusters, 81.1% residing among landraces within sub-clusters, and 1.9% within the landraces. The distribution pattern of genetic diversity among the sub-clusters of each cluster was uneven, with two HSuM sub-clusters （Central China） and some South China sub-clusters showing significantly higher level of genetic diversity.     

Genetic Diversity Analysis Among Populations of Mink from China by Inter-simple Sequence Repeat （ISSR） Markers

Inter-simple Sequence Repeat （ISSR） analysis was applied to assess the genetic diversity within and among five populations of mink from Liaoning Province. A total of 20 primers were screened, five selected primers produced 35 discernible bands, with 30 （85.71%） being polymorphic, indicating high genetic diversity at the species level. The highest genetic diversity was observed in the brown mink population, whereas the lowest diversity was found in the standard-pitchy mink population. Based on genetic distance （1972）, a dendrogram was constructed by using UPGMA algorithm, and five populations were divided into two major groups. Group I consisted of only the standard-pitchy mink population, and Group II included other four populations, in Group II, sapphire mink was close to brown mink population. The results of genetic differentiation indicated that the genetic differentiation degree between populations was lower and the genetic variation primarily came from within populations. This paper showed that ISSR technique was a reliable tool that could be used to study genetic diversity in the mink.     

A Comparative Analysis of B Chromosomes and Genetic Diversity in Maize （Zea mays L.） Landraces from Southwest China

The number of B chromosomes （Bs） in 54 maize landraces from Southwest China was tested by means of cytological observations. Nine landraces with Bs were observed. A map, showing the geographic distribution of the landraces with Bs, was plotted. It was found that southeastern Sichuan Province in China was the main distribution area of the landraces with Bs in Southwest China. In order to obtain information on relationships between Bs and genetic variation, genetic diversity both among and within 11 landraces was evaluated. For each SSR marker, the number of alleles ranged from 3 to 12 with an average of 7.86, which revealed a high level of genetic diversity among maize landraces in Southwest China. Based on SSRs data, higher genetic variation was found in the landraces with 2B, and the genetic distance between the landraces with and without Bs was higher. The results together with the principal component analysis （PCA） supported the hypothesis that maize landraces in Southwest China were first introduced to the middle part of southwest Sichuan, China. At the same time, the effect of Bs on genetic variation was discussed.     

Genetic Variation in Triticum turgidum L.ssp.turgidum Landraces from China Assessed by EST-SSR Markers

It was helpful for the wheat improvement to evaluate the genetic resources of Triticum turgidum L. ssp. turgidum landraces. In this study, 68 turgidum landraces accessions, belonging to four geographic populations in China, were investigated by using EST-SSR markers. A total of 63 alleles were detected on 22 EST-SSR loci, and the number of alleles on each locus ranged from 1 to 5, with an average of 2.9. The results of the analysis of molecular variance （AMOVA） indicated that 92.5% of the total variations was attributed to the genetic variations within population, whereas only 7.5% variations among populations. Although the four populations had similar genetic diversity parameters, Sichuan population was yet distinguished from other populations when comparing the population samples in pairs. Significant correlations were detected by the statistic analysis among six genetic diversity parameters among each other. The selection difference between heterozygosty and homozygosty was also observed among different EST-SSR locus. The genetic similarity （GS） ranged from 0.18 to 0.98, with the mean of 0.72, and all accessions could be clustered into 7 groups. The dendrogram suggested that the genetic relationships among turgidum accessions evaluated by EST-SSR markers were unrelated to their geographic distributions. These results implied that turgidum landraces from China had the unique characters of genetic diversity.     

ISSR-Based Molecular Characterization of an Elite Germplasm Collection of Sweet Potato （Ipomoea batatas L.） in China

To determine the genetic diversity and population structure of sweet potato accessions cultivated in China, and to establish the genetic relationships among their germplasm types, a representative collection of 240 accessions was analyzed using inter-simple sequence repeat （ISSR） markers. The mean genetic similarity coefifcient, Nei’s gene diversity, and shared allele distance of tested sweet potato accessions were 0.7302, 0.3167 and 0.2698, respectively. The 240 accessions could be divided into six subgroups and ifve subpopulations based on neighbor-joining （NJ） clustering and STRUCTURE results, and obvious genetic relationships among the tested sweet potato accessions were identiifed. The marker-based NJ clustering and population structure showed no distinct assignment pattern corresponding to lfesh color or geographical ecotype of the tested sweet potato germplasm. Analysis of molecular variance （AMOVA） revealed small but signiifcant difference between white and orange-lfeshed sweet potato accessions. Small but signiifcant difference were also observed among sweet potato accessions from the Southern summer-autumn sweet potato region, the Yellow River Basin spring and summer sweet potato region and the Yangtze River Basin summer sweet potato region. This study demonstrates that genetic diversity in the tested sweet potato germplasm collection in China is lower than that in some reported sweet potato germplasm collections from other regions. Pedigree investigations suggest that more diverse Chinese sweet potato varieties should be formed by broadening the selection scope of breeding parents and incorporating the introduced varieties into future breeding programs.     

The Eco-Geographical Distribution of Chemi-cal Composition of Soybean Seeds

The expression of protein and oil content of soybean seeds in worldwide was studied. The results shown that: Latitude and year's weather conditions affected protein content of soybean seeds importantly. Elevation affected oil content significantly. There was important difference in protein / oil content among different eco - geographical regions. The zone, in which there was the highest content of protein / oil, was that one with latitude from 0°to 20°59′ . And in this zone, there were different elevation regions, in which protein or oil content was the highest. For high pro-tein, it was the elevation region with 500 - 1000 m; for oil, it was 0~ 500 m. Protein / oil content was also different among different years. However, the changing range among years in Tropical and Subtropical regions was smaller than that in Temperate Regions. The relationship between protein / oil content and latitude, elevation or soil pH in the regions outside the Tropic of concerned a     

Broadening soybean genetic basis in the northeast of China

The bottle neek of advancement of soybean breeding inthe Northeast of China is the lack of genetic diversity of the parents used in cross breeding.In order to overcome this constrained condition,under the sponsorship of China National Committe of Natural Science Fundation,a network project with the topic“Broadening and Improving of the Genetic Basis of the Northeast Soybeans“ was established in 1990,and the Northeast agricultural University was apointed to take charge of the project.The project included the following four items:I.Breeding high yield and improved quality Northeast Soybeans,directed by Hcilongjiang Academy of Agricultural Sciencee .II.Development of new soybean gerplasms highly resistant to diseases epidemic in Northeast China directed by Northeast Agricultural University.Ⅲ.Exploitation of the potential of wild and semicultivated soybeans for broadening and improving the genetic basis of Northeast soybeans,directed by Jilin Academy of Agricultural Science.Ⅳ.Improving methods and technique for development of new soybean genetic resources.directed by Nanjing Agricultural University .Each item contained several research subjects conducted by research workers of different institutes of agricultural sicences.During the period 1991-1992.considerable promising new germplasms had been discovered or developed.The new germplasms not only possessed specific improved characters but also behaved with appropriate ecological types adapted to different conditions of Northeast.Among the numerous new germplasms developed.Gong Jio 8757-3 had a protein content of 49.41%,100 seed weight 16-17g,and acceptable agronomic characters,which was considered a very valuable new high protein content germplasm.Such developed new germplasma with enforced and imprved genetic basis will be used primarily as parents in soybean cross breeding.     

Cryptic species composition and genetic diversity within Bemisia tabaci complex in soybean in India revealed by mtCOI DNA sequence

Bemisia tabaci is a cryptic species complex, causing significant loss on many agriculturally important crops worldwide. Knowledge on species composition and diversity within B. tabaci complex is critical for evolving sustainable pest management strategies. Here we investigate the whitefly species complex in soybean in major soybean growing states of India. The mitochondrial cytochrome oxidase gene subunit-1(mt COI) based phylogenetic relationships established using Bayesian methods indicated the existence of three cryptic species namely AsiaⅠ, AsiaⅡ1, and AsiaⅡ7. All the haplotypes detected in the study could be assigned to these three cryptic species following the species demarcation criteria of 3.5% divergence threshold. Of these, AsiaⅡ1 was found to be predominant with wide spread distribution across the surveyed regions from cool temperate zones to hot and humid tropical plains. On the contrary, cryptic species AsiaⅡ7 showed localized distribution. The AsiaⅡ1 exhibited the highest haplotype diversity and AsiaⅠ showed high level of nucleotide diversity. There was a significantly high genetic differentiation among these three cryptic species. The MEAM 1, a dreadful invasive species was not detected in the specimens tested in the current study. The diversity and distribution of three cryptic species is discussed in the light of current knowledge on distribution of whitefly species in India and yellow mosaic disease observed during sampling survey.     

Genetic Variation in Rhizome Lotus （Nelumbo nucifera Gaertn. ssp. nucifera） Germplasms from China Assessed by RAPD Markers

To estimate genetic variation in rhizome lotus （Nelumbo nucifera Gaertn. ssp. nucifera） germplasms in China, a total of 94 rhizome lotus germplasms collected from 18 provinces in China were assessed. The RAPD （randomly amplified polymorphic DNA） marker was employed. The selected 17 random primers detected 139 polymorphic alleles out of a total 207 （67.15%）. Nei＇s gene diversity statistics and region differentiation parameters indicated that all germplasms had a relatively high level of genetic diversity with ne = 1.3202, h = 0.1937, I= 0.2982 and the gene flow among all regions was Nrn = 5.5742. The UPGMA dendrogram clustered all 94 germplasms into two clusters： One contained eight commercial cultivars and major landraces, and the other included the wild and some special landraces from five regions, and the PCA analysis exhibited the similar result. Those germplasms from southwestern and eastern China had higher genetic diversity than those from the southern, northern and central China. Predominant proportion of genetic variation （95.61%） was found significant within rather than among （4.39%） regions, as revealed by AMOVA analysis. The data analysis also revealed that the genetic diversity of rhizome lotus germplasms among different regions is positively related to their geographic distances, though it is ambiguous to find the trend from the UPGMA dendrogram and the PCA analysis. A relatively high genetic diversity and gene flow resided in the root lotus germplasms; about 96% of the variation was found within region; accessions from southwest and eastern China have higher genetic diversity than those from the southern, northern and central China.     

Dynamic Change of Genetic Diversity in Conserved Populations with Different Initial Genetic Architectures

Maintenance and management of genetic diversity of farm animal genetic resources (AnGR) is very important for biological, socioeconomical and cultural significance. The core concern of conservation for farm AnGR is the retention of genetic diversity of conserved populations in a long-term perspective. However, numerous factors may affect evolution of genetic diversity of a conserved population. Among those factors, the genetic architecture of conserved populations is little considered in current conservation strategies. In this study, we investigated the dynamic changes of genetic diversity of conserved populations with two scenarios on initial genetic architectures by computer simulation in which thirty polymorphic microsatellite loci were chosen to represent genetic architecture of the populations with observed heterozygosity (Ho) and expected heterozygosity (He), observed and mean effective number of alleles (Ao and Ae), number of polymorphic loci (NP) and the percentage of polymorphic loci (PP), number of rare alleles (RA) and number of non-rich polymorphic loci (NRP) as the estimates of genetic diversity. The two scenarios on genetic architecture were taken into account, namely, one conserved population with same allele frequency (AS) and another one with actual allele frequency (AA). The results showed that the magnitude of loss of genetic diversity is associated with genetic architecture of initial conserved population, the amplitude of genetic diversity decline in the context AS was more narrow extent than those in context AA, the ranges of decline of Ho and Ao were about 4 and 2 times in AA compared with that in AS, respectively, the occurrence of first monomorphic locus and the time of change of measure NP in scenario AA is 20 generations and 23 generations earlier than that in scenario AS, respectively. Additionally, we found that NRP, a novel measure proposed by our research group, was a proper estimate for monitoring the evolution of genetic diversity in a closed conserved population. Our study suggested that current managements of conserved populations should emphasize on initial genetic architecture in order to make an effective and feasible conservation scheme.     

Genetic Analysis of Embryo, Cytoplasm and Maternal Effects and Their Environment Interactions for Isoflavone Content in Soybean [Glycine max （L.） Merr.]

Soybean seed products contain isoflavones （genistein, daidzein, and glycitein） that display biological effects when ingested by humans and animals. These effects are species, dose and age dependent. Therefore, the content and quality of isoflavones in soybeans is a key factor to the biological effect. Our objective was to identify the genetic effects that underlie the isoflavone content in soybean seeds. A genetic model for quantitative traits of seeds in diploid plants was applied to estimate the genetic main effects and genotype x environment （GE） interaction effects for the isoflavone content （IC） of soybean seeds by using two years experimental data with an incomplete diallel mating design of six parents. Results showed that the IC of soybean seeds was simultaneously controlled by the genetic effects of maternal, embryo, and cytoplasm, of which maternal genetic effects were most important, followed by embryo and cytoplasmic genetic effects. The main effects of different genetic systems on IC trait were more important than environment interaction effects. The strong dominance effects on isoflavone from residual was made easily by environment conditions. Therefore, the improvement of the IC of soybean seeds would be more efficient when selection is based on maternal plants than that on the single seed. Maternal heritability （65.73%） was most important for IC, followed by embryo heritability （25.87%） and cytoplasmic heritability （8.39%）. Based on predicated genetic effects, Yudou 29 and Zheng 90007 were better than other parents for increasing IC in the progeny and improving the quality of soybean, The significant effects of maternal and embryo dominance effects in variance show that the embryo heterosis and maternal heterosis are existent and uninfluenced by environment interaction effects.     

Analysis of SSR Fingerprints in Introduced Silkworm Germplasm Resources

Thirty-five SSR markers were used to construct 96 silkworm races fingerprint. All the SSR markers were polymorphic and unambiguously separated silkworm strains from each other. A total of 467 alleles were detected with a mean value of 13.34 alleles/locus （range 3-28）. The mean polymorphism index content （PIC） was 0.71 （range 0.299-0.919）. UPGMA cluster analysis of Nei＇s genetic distance grouped silkworm strains on the basis of their origin. The results indicated that SSR markers are efficient tools for fingerprinting cultivars and conducting genetic diversity studies in the silkworm.     

Genetic Diversity and Evolutionary Tendency Detected by Isozyme, RFLP and RAPD Markers in the Wild and Cultivated Soybean in China

A large numbers of samples of wild soybean accessions and cultivated soybean landraces from various areas in China were analyzed by isozyrme, cytoplasmic DNA RFLP and nuclear DNA RAPD markers in order to reveal their genetic diversity. Greater comprehensive genetic diversity was detected in wild soybean than in cultivated soybean. The genetic plentifulness and the genetic dispersion of wild soybean were 180 (95. 2％) and 0. 2891 while those of cultivated soybean were 154(81.5％) and 0. 2091,respectively. On the most loci, especially on isozyme loci Idh1, Aph, Idh2,and Dia, cytoplasmic DNA RFLP loci cp Ⅰ , cp Ⅲ, mt Ⅳ a and mt Ⅳ b, and nuclear RAPD loci OPAP4-8, OPAP5-1, OPAP9-8 and OPAP20-8, the wild soybeans djffered remarkably from the cultivated ones in allele frequency. These markers could be used in further study on the evolution and origin of the cultivated soybean.     

Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm

Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium（LD）. This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism（PIC=0.53） was found, and three groups were detected（K=3） with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model（GLM） and mixed linear model（MLM）（P 0.01）. The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci（QTLs） information for marker-assisted selection.     

Genetic Differentiation Analyses Based on mtDNA COⅡ Gene Sequences Among Different Geographic Populations of Aphis glycines(Hemiptera: Aphididae) in Northeast China

Aphis glycines(Hemiptera: Aphididae) is considered as a cosmopolitan pest of cultivated soybean, major diffi culties in its control measures may be due to its higher genetic diversity; however, the knowledge about population genetic diversity of this species is limited. This study aimed to represent the genetic differentiation among different geographic populations of soybean aphid in Northeast China. In order to investigate and assess the genetic diversity, genetic differentiation, molecular variance, population structure, ecological importance and evolutionary history of A. glycines, we sequenced a fragment of one protein-coding gene, the cytochrome c oxidaseⅡof mitochondrial DNA gene. The results showed that four haplotypes were defi ned among COⅡ gene of 180 sequences of soybean aphid in Northeast China including H1 shared by all the populations. Lower haplotype diversity(Hd=0.3590±0.0420) and nucleotide diversity(Pi=0.0012±0.0002) were observed and high gene flow was detected in every two populations, while most of the variation(80.81%) arose from variability within A. glycines from individuals. Low genetic differentiation and high gene fl ow(Nm=2.106) indicated a high migration rate between the populations, which might reveal that gene flow in different geographic populations did not affect by geographical distance. The phylogenetic tree and the haplotype network of A. glycines were obtained based on sequences of COⅡ gene, there were no signifi cant genealogical branches or clusters recognized in NJ tree, and no clear distribution, delineation of haplotypes were demonstrated in the haplotype network according to geographical location. This study rejected the vicariance hypothesis: geographic isolation could be a barrier and it restricted A. glycines gene fl ow among 10 populations.     

Comparative Analysis of Genetic Diversity in Landraces of Waxy Maize from Yunnan and Guizhou Using SSR Markers

Waxy maize landraces are abundant inYunnan and Guizhou of China. Genetic diversity of waxy maize landraces from Yunnan and Guizhou were analyzed using SSR markers. We screened 38 landraces with 50 primers that generated 3 to 6 polymorphic bands, with an average of 4.13 bands. Shannon＇s information indices for genetic diversity of the 14 waxy maize landraces from Yunnan varied from 4.9571 to 42.1138 and averaged 26.5252; Shannon＇s information indices for genetic diversity of the 24 waxy maize landraces from Guizhou varied from 22.0066 to 40.6320 and averaged 32.3156. For the 14 waxy maize landraces from Yunnan, the within-landrace genetic diversity accounted for 45.40% and the among-landrace genetic diversity accounted for 54.60% of the total genetic diversity observed. For the 24 waxy maize landraces from Guizhou, the within-landrace genetic diversity accounted for 50.76% and the among-landrace genetic diversity accounted for 49.24% of the total observed. Some individual landraces possessed as much as 96.86% of the total genetic diversity occurring among landraces within origins. Differentiation between geographic origins accounted for only 3.14% of the total genetic diversity. Both Yunnan and Guizhou would be the diversity centers and the original centers of waxy maize.     

Analysis of Genetic Diversity and Relationships of Seven Chinese Indigenous Pig Breeds and Three Exotic Pig Breeds Using the DNA Differential Display Technique

The genetic diversity and relationships of seven Chinese indigenous pig breeds （Meishan, Erhualian, Hezuo, Bamei, Qingping, Tongcheng, and Huainan） and three exotic pig breeds （Large White, Landrace, and Duroc） were analyzed using the DNA differential display technique by means of eight primer combinations. A total of 123 reproducible bands were used to calculate mean Nei＇s gene diversity, and mean Shannon＇s information index for each pig population. Based on these the Nei＇s standard genetic identity and distance were estimated, which was used to construct a dendrogram tree for the 10 pig breeds. The experimental results obtained and the method used in this study for evaluating the genetic diversity and relationships of pigs were also discussed.