Genetic linkage mapping and QTL identification for salinity tolerance in Indian mustard(Brassica juncea L.Czern and Coss.)using SSR markers

Soil salinity is one of the major environmental constraints that limits crop yield and nearly 7%of the total area worldwide is affected by salinity.Salinity-induced oxidative stress causes membrane damage during germination and seedling growth.Indian mustard is a major oilseed crop in India and its production and productivity are severely affected by salt stress.Breeding Brassica cultivars for salinity tolerance by conventional means is very difficult and time-consuming.Therefore,understanding the molecular components associated with salt tolerance is needed to facilitate breeding for salt tolerance in Brassica.In this investigation,quantitative trait loci(QTLs)associated with salt tolerance were identified using F_(2:3)mapping population developed from a cross between CS52(salinity tolerant)and RH30(salinity sensitive).Parents and F_(2:3)were evaluated under controlled and salinity stress conditions for 14 morpho-physiological traits for two consecutive generations(F2 and F_(2:3)),explaining proportion of the phenotypic variance under control condition.Simple sequence repeat(SSR)markers were used for mapping studies.A genetic linkage map based on 42 simple sequence repeats(SSRs)markers was constructed covering 2298.5 cM(Haldane)to identify the loci associated with salt tolerance in Brassica juncea.Forty-one SSRs showing polymorphism in the parents(CS52 and RH30)were mapped on 8 linkage groups(C1–C8).One marker(nga 129)did not map to any of the linkage group and was excluded from mapping.Linkage group 5(C5;317.9 cM)was longest and linkage group 1(C1,255.0 cM)was shortest.Further,we identified 15 QTLs controlling 8 traits using F_(2:3)population.These QTLs explained 12.44–60.63%of the phenotypic variation with a LOD score range of 3.62–5.97.Out of these QTLs,QMI4.1 related to membrane injury showed 51.28%phenotypic variance with a LOD score of 3.34.QTL QBYP8.1 related to biological yield per plant showed 60.63%phenotypic variance at a LOD score of 3.62.The highest LOD score of 5.97 was recorded for QTL related to seed yield per plant(QSYP4.1).Major QTLs were QTL for biological yield per plant(QBYP8.1),QTL for siliquae per plant(QSP4.1),QTL for primary branches(QPB4.1),QTLs for seed per siliqua(QSS4.1,QSS4.2),QTL for seed yield per plant(QSYP4.1),and QTL for membrane injury(QMI8.1)which showed more than 50%phenotypic variance.These QTLs identified in our study need to be confirmed in other populations as well so that these can be used in marker-assisted selection and breeding to enhance salt tolerance in Brassica juncea.

Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq

Carex rigescens(Franch.) V.Krecz is a wild turfgrass perennial species in the Carex genus that is widely distributed in salinised areas of northern China.To investigate genome-wide salt-response gene networks in C.rigescens,transcriptome analysis using high-throughput RNA sequencing on C.rigescens exposed to a 0.4% salt treatment(Cr_Salt) was compared to a non-salt control(Cr_Ctrl).In total,57 742 546 and 47 063 488 clean reads were obtained from the Cr_Ctrl and Cr_Salt treatments,respectively.Additionally,21 954 unigenes were found and annotated using multiple databases.Among these unigenes,34 were found to respond to salt stress at a statistically significant level with 6 genes up-regulated and 28 downregulated.Specifically,genes encoding an EF-hand domain,ZFP and AP2 were responsive to salt stress,highlighting their roles in future research regarding salt tolerance in C.rigescens and other plants.According to our quantitative RT-PCR results,the expression pattern of all detected differentially expressed genes were consistent with the RNA-seq results.Furthermore,we identified 11 643 simple sequence repeats(SSRs) from the unigenes.A total of 144 amplified successfully in the C.rigescens cultivar Lüping 1,and 69 of them reflected polymorphisms between the two genotypes tested.This is the first genome-wide transcriptome study of C.rigescens in both salt-responsive gene investigation and SSR marker exploration.Our results provide further insights into genome annotation,novel gene discovery,molecular breeding and comparative genomics in C.rigescens and related grass species.

Fingerprinting 146 Chinese chestnut(Castanea mollissima Blume)accessions and selecting a core collection using SSR markers

Chinese chestnut is an important nut tree around the world.Although the types of Chinese chestnut resources are abundant,resource utilization and protection of chestnut accessions are still very limited.Here,we fingerprinted and determined the genetic relationships and core collections of Chinese chestnuts using 18 fluorescently labeled SSR markers generated from 146 chestnut accessions.Our analyses showed that these markers from the tested accessions are highly polymorphic,with an average allele number(N_(a))and polymorphic information content(PIC)of 8.100 and 0.622 per locus,respectively.Using these strongly distinguishing markers,we successfully constructed unique fingerprints for 146 chestnut accessions and selected seven of the SSR markers as core markers to rapidly distinguish different accessions.Our exploration of the genetic relationships among the five cultivar groups indicated that Chinese chestnut accessions are divided into three regional type groups:group I(North China(NC)and Northwest China(NWC)cultivar groups),group II(middle and lower reaches of the Yangtze River(MLY)cultivar group)and group III(Southeast China(SEC)and Southwest China(SWC)cultivar groups).Finally,we selected 45 core collection members which represent the most genetic diversity of Chinese chestnut accessions.This study provides valuable information for identifying chestnut accessions and understanding the phylogenetic relationships among cultivar groups,which can serve as the basis for efficient breeding in the future.

SSR markers development and their application in genetic diversity evaluation of garlic(Allium sativum)germplasm

Garlic(Allium sativum),an asexually propagated vegetable and medicinal crop,has abundant genetic variation.Genetic diversity evaluation based on molecular markers has apparent advantages since their genomic abundance,environment insensitivity,and non-tissue specific features.However,the limited number of available DNA markers,especially SSR markers,are insufficient to conduct related genetic diversity assessment studies in garlic.In this study,4372 EST-SSR markers were newly developed,and 12 polymorphic markers together with other 17 garlic SSR markers were used to assess the genetic diversity and population structure of 127 garlic accessions.The averaged polymorphism information content(PIC)of these 29 SSR markers was 0.36,ranging from 0.22 to 0.49.Seventy-nine polymorphic loci were detected among these accessions,with an average of 3.48 polymorphic loci per SSR.Both the clustering analyses based on either the genotype data of SSR markers or the phenotypic data of morphological traits obtained genetic distance divided the 127 garlic accessions into three clusters.Moreover,the Mantel test showed that genetic distance had no significant correlations with geographic distance,and weak correlations were found between genetic distance and the phenotypic traits.AMOVA analysis showed that the main genetic variation of this garlic germplasm collection existed in the within-population or cluster.Results of this study will be of great value for the genetic/breeding studies in garlic and enhance the utilization of these garlic germplasms.

Development and application of perfect SSR markers in cotton

Background:This study aimed to develop a set of perfect simple sequence repeat(SSR)markers with a single copy in the cotton genome,to construct a DNA fingerprint database suitable for authentication of cotton cultivars.We optimized the polymerase chain reaction(PCR)system for multi-platform compatibility and improving detection efficiency.Based on the reference genome of upland cotton and 10×resequencing data of 48 basic cotton germplasm lines,single-copy polymorphic SSR sites were identified and developed as diploidization SSR markers.The SSR markers were detected by denaturing polyacrylamide gel electrophoresis(PAGE)for initial screening,then fluorescence capillary electrophoresis for secondary screening.The final perfect SSR markers were evaluated and verified using 210 lines from different sources among Chinese cotton regional trials.Results:Using bioinformatics techniques,1246 SSR markers were designed from 26626 single-copy SSR loci.Adopting a stepwise(primary and secondary)screening strategy,a set of 60 perfect SSR markers was selected with high amplification efficiency and stability,easy interpretation of peak type,multiple allelic variations,high polymorphism information content(PIC)value,uniform chromosome distribution,and single-copy characteristics.A multiplex PCR system was established with ten SSR markers using capillary electrophoresis detection.Conclusions:A set of perfect SSR markers of cotton was developed and a high-throughput SSR marker detection system was established.This study lays a foundation for large-scale and standardized construction of a cotton DNA fingerprint database for authentication of cotton varieties.

Research in migration route of hatchery released Chinese shrimp(Fenneropenaeus chinensis) in the Bohai Bay using method of SSR marker

This study provides new insights for the hatchery released Chinese shrimp(Fenneropenaeus chinensis),including proportion,dynamic migration route,after they were released into nature for stock enhancement using a new strategy quite different than ever.Chinese shrimp were sampled at 22 survey stations during two investigation voyages acrossing 74 survey stations in the Bohai Sea from July 16 to August 9 in 2015.Among 289 sampled individuals during the second voyage,totally 155 shrimps were identified as hatchery shrimp released into the Laizhou Bay at mid-May in 2015 based on finger-print of eight SSR(simple sequence repeats)markers,and the proportion of hatchery released shrimp in recapture samples were from 41.30%–85.71%in each station with an average value 53.63%,which verified a previous view point that up to 90%of autumn season Chinese shrimp landing in the Bohai Sea were composed of hatchery released.Meanwhile,the dynamic migration route of hatchery released shrimp revealed that part of released shrimp migrated heading northwest along the west coast of the Bohai Sea up to the Bohai Bay but just remained at the Laizhou Bay until over-wintering migration at midOctober when they initiate over-wintering migration.Present unnatural spring season shrimp fishing model cut the throat of spawner shrimp chance to swim back to their respective spawning plants at each spring,it still no chance to clarify whether the hatchery released shrimp could replenish to the reproduce population and complete a whole life cycle as same as their natural relatives.

Development of polymorphic SSR markers and their applicability in genetic diversity evaluation in Euptelea pleiosperma

Euptelea pleiosperma is a characteristic species of East Asian flora with both ornamental and scientific values.Based on the reduced-representation sequencing(RRS)technology of RAD-Seq,this study conducted high-throughput Illumina paired-end sequencing to find SSR marker information in the genome of E.pleiosperma,and to screen and verify polymorphism of SSR markers.We obtained 5.5G of high-quality data using RAD-Seq.The total number of contigs of the RAD tags was 299,376,with the maximum contig length of 2,062 bp and the average length of 445 bp.From these sequences,we identified 20,718 SSR loci,with a distribution density of one SSR per 6.45 kb(1/6.45 kb).Among all SSRs,dinucleotides(52.00%)were the most detected SSRs,followed by mononucleotides(21.63%).AG/CT was the dominant motif in the SSR loci,accounting for 34.8%.Primers were successfully designed for 14,593 loci,and 100 pairs of these primers were randomly selected for chemical synthesis and validated by SSR-PCR amplification in 20 individuals of E.pleiosperma.Seventy-nine primers were able to amplify the target bands.Cervus 3.0 software was used to analyze the selected 20 SSR loci with good polymorphism.For the 20 SSR markers,the number of alleles ranged from 4 to 9,and the observed heterozygosity and expected heterozygosity were from 0.35 to 0.75 and 0.541 to 0.875,respectively.The information content of polymorphic loci ranged from 0.463 to 0.848,with an average value of 0.638.Among them,there were 18 highly polymorphic loci,and 20 SSR loci did not deviate from the Hardy-Weinberg equilibrium.Furthermore,the 20 pairs of SSR primers were used to conduct PCoA analysis based on Nei’s genetic distance of 51 individuals from three populations.The results showed that these SSR markers could distinguish genetic differences based on different geographical locations.

Multiplex PCR System Optimization with Potato SSR Markers

Potato variety Kexin18 was used as testing materials in this research to study the influence on main components in multiplex PCR system,different primer ratios and annealing temperatures in SSR marker amplification.Concentration and gradient experiments for four components(enzyme,MgCl2,DNA template and dNTPs) in PCR system were used in the research with the concentration of the other component remained the same;the orthogonal design L9(34) was applied in the optimization of four sets of primers(STM0014,Pat,SSI,and UGP) in the reaction system at three levels;the temperature gradient selection was used to find out the optimum annealing temperature for the primer.The optimized multiplex PCR system of potato SSR marker with a total volume of 20 μL:2.5 μL 25 mmol · L-1 MgCl2,0.6 μL 10 mmol · L-1 dNTPs,0.8 U Taq,80 ng DNA template was ultimately established through the comparison and analysis of test results;the ratio of four pairs of 4 mmol · L-1 primers was 2:1:2:3,and the annealing temperature was 54.7℃.The optimized reaction system could be repeated stably;and the stable and reliable amplification results were able to clearly distinguish different potato varieties.This research built the solid foundation for the further study of genetic diversity of potato germplasms and construction of DNA fingerprinting..

Identification of Co-dominant SSR Markers Associated with Genes Controlling α'- and cr-subunit-null β-conglycinin Phenotypes in Soybean (Glycine max (L.) Merr.)

Studies have shown that the three subunits of β-conglycinin are the main potential allergens of soybean sensitive patients.And β-conglycinin has adverse effects on nutrition and food processing.So solation and production of lines with lowerβ-conglycinin content has been the focus of recent soybean breeding projects.Soybean lines with deficiency in one or all subunits of β-congIycinin have been obtained.An effective and rapid system to identify such mutations will facilitate genetic manipulation of the β-conglycinin subunit composition.Here,two segregating F2 populations were developed from crosses between Cgy-1/cgy-1(CC),anα'-lacking line(△α'),and DongNong 47(DN47),a wild-type(Wt)Chinese soybean cultivar with normal globulin components,and Cgy-2/cgy-2(CB),an a-lacking line(△α),and DN47.These populations were used to estimate linkage among the egy-1(conferring α'-null)and cgy-2(α-null)loci and simple sequence repeat(SSR)markers.Seven SSR markers(Sat_038,Satt243,Sat_307,Sat_109,Sat_231,Sat_108 and Sat_190)were determined to co-scgregate with cgy-1,and six SSR markers(Satt650,Satt671,Sat_418,Sat_170,Satt292 and Sat_324)co-segregated with cgy-2.Linkage maps being composed of seven SSR markers and egy-1 locus,and six SSR markers and the cgy-2 locus were then constructed.It assigned that the egy-1 gene to chromosome 10 at a position between Sat_307 and Sat_231,and the cgy-2 gene to chromosome 20 at a position between Satt650 and Satt671.These markers should enable map-based cloning of the egy-1 and cgy-2 genes.For different subunit-deficiency types[α'-null,α-null and(α'+α)-null types],the two sets of SSR markers could also detect of polymorphism between three normal cultivars and seven related mutant lines.The identification of these markers is great significance to the molecular marker-assisted breeding of soybean/9-conglycinin subunits.

Identification of Introgressed Lines by the SSR Markers and Agronomic Traits

The wild cotton cultivars and species have abundant genetic polymorphisms,and they possess lots of excellent genes,such as drought resistance,insect resistance,fine and strong fiber,and so on.

Selection of Tolerant of Some Citrus Hybrids F1 to Calcareous Stress and Identification Sexuall Individuals by SSR Marker

The research was conducted during two seasons 2018-2019 and 2019-2020, at the Scientific Research Center in Lattakia-Syria, where the cross between Sour orange, Cleopatra mandarin and Trifoliate orange. The first season was (Sour orange ♂ × Cleopatra mandarin ♀) and (Cleopatra mandarin ♂ × sour orange ♀) and (sour orange ♂ × trifoliate orange ♀), and the crossing in the second season was (Trifoliate orange ♂ × Sour orange ♀), and (Trifoliate orange ♂ × Cleopatra mandarin ♀). The plants of the first generation F1 were exposed to calcareous stress according to two methods. The first one for a long term (two years) method was grown in plots containing 15% and 35% Calcium Carbonate and the control free of Calcium Carbonate for the first cross, and the second one short term (two months) by watering method was with a solution of 1 mol and 2 mol of Calcium Carbonate for the second cross. The indicators of proline and chlorophyll A, B and T were measured in the first-generation individuals, once at the beginning of the experiment and a second time at the end of study. Seven SSR primers were used to identify sexual individuals, five primers were able to identify sexual F1 individuals are CSM13, CSM17, CSM147, CSM18 and TAA27, F1 individuals in the first season (mixture experiment) gave high values of chlorophyll and were tolerant to calcareous stress from crossing Cleopatra mandarin and Sour orange, where they did not show a deterioration in chlorophyll, but rather increased chlorophyll values, and the Trifoliate orange hybrids were sensitive to this stress, and in the watering experiment the F1 showed significant deterioration in Chlorophyll in all seedlings, and symptoms of Lime-induced chlorosis appeared on the more sensitive seedlings.

Bulked Segregant Analysis to Detect QTL Related to Heat Tolerance in Rice(Oryza sativa L.) Using SSR Markers

The study was undertaken to assess the genetic effect of quantitative trait loci(QTLs) conferring heat tolerance at flowering stage in rice.A population consisting of 279 F2 individuals from the cross between 996,a heat tolerant cultivar and 4628,a heat-sensitive cultivar,was analyzed for their segregation pattern of the difference of seed set rate under optimal temperature condition and high temperature condition.The difference of seed set rate under optimal temperature condition and high temperature condition showed normal distribution,indicating the polygenic control over the trait.To identify main effect of QTL for heat tolerance,the parents were surveyed with 200 primer pairs of simple sequence repeats(SSR).The parental survey revealed 30% polymorphism between parents.In order to detect the main QTL association with heat tolerance,a strategy of combining the DNA pooling from selected segregants and genotyping was adopted.The association of putative markers identified based on DNA pooling from selected segregants was established by single marker analysis(SMA).The results of SMA revealed that SSR markers,RM3735 on chromosome 4 and RM3586 on chromosome 3 showed significant association with heat tolerance respectively,accounted for 17 and 3% of the total variation respectively.The heat tolerance during flowering stage in rice was controlled by multiple gene.The SSR markers,RM3735 on chromosome 4 and RM3586 on chromosome 3 showed significant association with heat tolerance respectively,accounted for 17 and 3% of the total variation respectively.The two genetic loci,especially for RM3735 on chromosome 4,can be used in marker-assistant-selected method in heat tolerance breeding in rice.

Detection of Allelic Variation in Chinese Wheat (Triticum aestivum L.) Germplasm with Drought ToleranceUsing SSR Markers

Allelic variation in two domestic wheat landraces, Pingyaobaimai and Mazhamai, two cornerstone breeding materials and their derived cultivars with drought tolerance was detected by SSR (simple sequence repeat) markers. The clustering of 25 accessions showed that the similarity between Pingyaobaimai and Yanda1817, the latter was developed from the former, was 0.71, the highest one of all accessions, but the similarities were very low between these two accessions and other accessions including their derived cultivars. A similar situation was revealed between Mazhamai and its derived cultivars. Pingyaobaimai and its three derived cultivars shared three alleles at loci Xgwm526, Xgwm538 and Xgwm126 on chromosome arms 2BL, 4BL and 5AL, respectively. There were six shared alleles in Mazhamai and its derived cultivars, in order of Xgwm157,Xgwm126, Xgwm212, Xgwm626, Xgwm471 and Xgwm44 on chromosome arms 2DL, 5AL, 5DL, 6BL, 7AS and 7DC, respectively. Only one shared allele was detected between the pedigrees of Pingyaobaimai and Mazhamai. The difference of shared alleles in two cornerstone breeding materials and their derived cultivars revealed the diversity in Chinese wheat germplasm with drought tolerance and the complication in genetic basis of drought tolerance in wheat.

Genetic Analysis and Preliminary Mapping of a Highly Male-Sterile Gene in Foxtail Millet(Setaria italica L.Beauv.) Using SSR Markers

Breeding of male-sterile lines has become the mainstream for the heterosis utilization in foxtail millet,but the genetic basis of most male-sterile lines used for the hybrid is still an area to be elucidated.In this study,a highly male-sterile line Gao146A was investigated.Genetic analysis indicated that the highly male-sterile phenotype was controlled by a single recessive gene a single recessive gene.Using F2population derived from cross Gao146A/K103,one gene controlling the highly malesterility,tentatively named as ms1,which linked to SSR marker b234 with genetic distance of 16.7 cM,was mapped on the chromosome VI.These results not only laid the foundation for fine mapping of this highly male-sterile gene,but also helped to accelerate the improvement of highly male-sterile lines by using molecular marker assisted breeding method.

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.

Assessment of wheat variety distinctness using SSR markers

Assessment of variety distinctness is important for both the registration and the protection of particular variety. However, the current testing system, which assesses a range of morphological characters of each pair of varieties grown side-by-side, is time-consuming and is not suitable for the assessment of hundreds of samples. The objective of this study was to develop a procedure for the assessment of wheat variety distinctness using simple sequence repeat(SSR) markers. A comparison between the molecular and morphological profile of 797 varieties was made. On the basis of the comparison, pairs of varieties with a genetic similarity value(GSV) ≤90% were deemed to be distinct, accounting for ~85% of varieties assessed in wheat regional trials. For the remaining ~15% of varieties, GSVs between different varieties were >90%, among which ~35% were not distinct and the other ~65% were distinct. Therefore, if given a GSV>90%, the pairs of varieties should be morphologically assessed in the field. To avoid any errors in the assessments, we proposed the elimination of contaminant plants from the sample before comparing the varietal genotypes, scoring of the genotype at each locus with a pair of allele numbers when constructing a molecular profile, and faithfully recording two alleles at a non-homozygous locus. To reduce the workload and cost, a three-grade markers comparison among varieties is suggested. In addition, 80 SSR markers and a technical procedure for assessment of wheat variety distinctness have been proposed. Based on the procedure, the distinctness assessment of ~85% of all wheat varieties is completed in our laboratory annually. Consequently, total field assessment has been reduced considerably.

SSR Markers for Fusarium Head Blight Resistance QTLs in Three Wheat Populations

The objective of this research is to identify DNA markers linked to QTLs controlling FHB resistance in wheat, and to compare if the QTLs in three resistant germplasm are common. Three wheat recombinant inbred populations derived from the crosses between Alondra (susceptible) and three resistant lines, Wangshuibai, Sumai3, and 894037, respectively, were evaluated for reaction to Fusarium graminearum in greenhouse and in field conditions over years. Simple sequence repeat (SSR) markers were screened in the populations and regression analysis was used to identify markers associated with FHB resistance. For the population of Sumai3 (resistant)/Alondra (susceptible), which contained 161 recombinant inbred lines, two SSR markers located on chromosome 3B were found to be associated with resistant QTLs. These markers accounted for 2.66.7% phenotypic variation. The 894037 (resistant)/Alondra (susceptible) population was consisted of 147 recombinant inbred lines. A total of 59 SSR primers were screened in this population and seven of them were linked to resistant QTLs. The QTLs on chromosome 3B accounted for 47.4% phenotypic variation. Minor QTLs were also located on 2D, 7A, 6B, and 4B chromosomes, and the resistant QTLs on 2D and 4B chromosomes were from Alondra. The last population of 80 recombinant inbred lines was from the cross Wangshuibai (resistant)/Alondra (susceptible). A total of 120 SSR primers were screened in this population, eight of which were linked to resistant QTLs. These markers were located on 3B, 4B, 2D, 4D, and 6D (uncertain) chromosomes respectively. The QTLs on chromosome 3B accounted for 8.927.0% phenotypic variation. The resistant QTLs on chromosomes 4B and 6D (uncertain) were from Alondra. The other QTLs were from Wangshuibai. SSR markers linked to resistant QTLs on chromosome 3B were found in all three populations, and account for higher phenotypic variation. So these markers should be useful in marker assisted selection.

Analysis of an Applied Core Collection of Adzuki Bean Germplasm by Using SSR Markers

Genetic diversity of 158 accessions of an applied core collection of adzuki bean (Vigna angularis) and 18 wild genotypes were assessed by using 85 microsatellite markers. With an average of 5.81 alleles per locus, 493 alleles were detected, and their distribution frequencies lower than 5% accounted for 73.02% of the total number. The distributions of alleles between the cultivated and the wild adzuki bean germplasm are different, with a higher allelic diversity in the wild germplasm than that of the cultivated ones. An obvious genetic differentiation was also observed between the wild and the cultivated adzuki beans, and SSR markers may be useful in study identification and classification of them. Among cultivated adzuki bean, the genetic similarity coefficient varied from 0.366 to 0.939. Genetic structure analysis can clearly separate the wild genotypes from the cultivated adzuki bean, and also can divide the cultivated ones into different populations, as these populations are closely agreeable with the ecological regions where they originally grow. The results of this study will be useful in arranging local breeding programs, especially in the aspect of parental combinations or identification of progenies. These SSR markers can also provide important information to explain the genetic relationship between the cultivated and wild adzuki beans, and to accelerate the wild gene resources in broadening the gene pool in breeding program.

Genetic Diversity of Maize Populations Developed by Two Kinds of Recurrent Selection Methods Investigated with SSR Markers

Two cycles of biparental mass selection (MS) and one cycle of half-sib-S3 family combining selection (HS-S3) for yield were carried out in 2 synthetic maize populations P4C0 and P5C0 synchronously. The genetic diversity of 8 maize populations,including both the basic populations and their developed populations,were evaluated by 30 SSR primers. On the 30 SSR loci,a total of 184 alleles had been detected in these populations. At each locus,the number of alleles varied from 2 to 14,with an average of 6.13. The number and ratio of polymorphic loci in both the basic populations were higher than those of their developed populations,respectively. There was nearly no difference after MS but decreased after HS-S3 in both the basic populations in the mean gene heterozygosity. The mean genetic distance changed slightly after MS but decreased in a bigger degree after HS-S3 in both the basic populations. Analyses on the distribution of genetic distances showed that the ranges of the genetic distance were wider after MS and most of the genetic distances in populations developed by HS-S3 were smaller than those in both the basic populations. The number of genotypes increased after MS but decreased after HS-S3 in both the basic populations. The genetic diversity of intra-population was much more than genetic diversity of inter-population in both the basic populations. All these indexes demonstrated that the genetic diversity of populations after MS was similar to their basic populations,and the genetic diversity was maintained during MS,whereas the genetic diversity of populations decreased after HS-S3. This result indicated that heterogeneity between some of the individuals in the developed populations increased after MS,whereas the populations become more homozygotic after HS-S3.

Association analysis of grain traits with SSR markers between Aegilops tauschii and hexaploid wheat(Triticum aestivum L.)

Seven important grain traits, including grain length(GL), grain width(GW), grain perimeter(GP), grain area(GA), grain length/width ratio(GLW), roundness(GR), and thousand-grain weight(TGW), were analyzed using a set of 139 simple sequence repeat(SSR) markers in 130 hexaploid wheat varieties and 193 Aegilops tauschii accessions worldwide. In total, 1 612 alleles in Ae. tauschii and 1 360 alleles in hexaploid wheat(Triticum aestivum L.) were detected throughout the D genome. 197 marker-trait associations in Ae. tauschii were identified with 58 different SSR loci in 3 environments, and the average phenotypic variation value(R2) ranged from 0.68 to 15.12%. In contrast, 208 marker-trait associations were identified in wheat with 66 different SSR markers in 4 environments and the average phenotypic R2 ranged from 0.90 to 19.92%. Further analysis indicated that there are 6 common SSR loci present in both Ae. tauschii and hexaploid wheat, which are significantly associated with the 5 investigated grain traits(i.e., GA, GP, GR, GL, and TGW) and in total, 16 alleles derived from the 6 aforementioned SSR loci were shared by Ae. tauschii and hexaploid wheat. These preliminary data suggest the existence of common alleles may explain the evolutionary process and the selection between Ae. tauschii and hexaploid wheat. Furthermore, the genetic differentiation of grain shape and thousand-grain weight were observed in the evolutionary developmental process from Ae. tauschii to hexaploid wheat.