Genetic diversity of African maize inbred lines revealed by SSR markers

Knowledge of genetic diversity (GD) and relationships among maize inbred lines is indispensable in a breeding program. Our objectives were to (1) investigate the level of genetic diversity among maize inbred lines and (2) assess their genetic structures by applying simple sequence repeat (SSR) markers. Fifty-six highland and mid-altitude maize inbred lines obtained from CIMMYT programs in Ethiopia and Zimbabwe were genotyped using 27 SSR loci. All of the genotypes studied could unequivocally be distinguished with the combination of the SSRs used. In total, 104 SSR alleles were identified, with a mean of 3.85 alleles per locus. The average polymorphism information content (PIC) was 0.58. GD expressed as Euclidean distance, varied from 0.28 to 0.73 with an average of 0.59. Cluster analysis using unweighted pair group method with arithmetic average (UPGMA) suggested five groups among the inbred lines. Most of the inbred lines adapted to the highlands and the mid-altitudes were positioned in different clusters with a few discrepancies. The pattern of groupings of the inbred lines was mostly consistent with available pedigree information. The variability detected using SSR markers could potentially contribute towards effective utilization of the inbred lines for the exploitation of heterosis and formation of genetically diverse source populations in Ethiopian maize improvement programs.     

Application of simple sequence repeat (SSR) markers for molecular diversity and heterozygosity analysis in maize inbred lines

There is an important role of understanding the genetic diversity among and within inbred lines at the molecular level for maize improvement in different breeding programs. The present study was devoted to estimate the level of genetic diversity among the inbred lines of maize using the simple sequence repeat analysis (SSR). The application of six different SSR markers successfully provided the information on similarity or diversity as well as the heterozygosity of the allelic loci for all the eight inbred line of maize.     

Genetic analysis of maize germplasm in the Korean Genebank and association with agronomic traits and simple sequence repeat markers

We assessed genetic and phenotypic variation in 105 maize germplasm accessions from RDA-Genebank of Korea and performed association analyses for 11 agronomical traits and 100 simple sequence repeats (SSR). Genetic diversity (GD) analysis revealed a total of 1104 alleles at the 100 SSR loci. The average number of alleles per locus was 11.0. The average GD and polymorphic information content values were 0.73 and 0.70, respectively. The average major allele frequency was 0.41. Population structure analysis indicated that these maize accessions comprised two major groups and one admixed group based on a membership probability threshold of 0.80. The two major groups contained 35 and 46 maize accessions. A mixed linear model of association analysis revealed five marker-trait associations with a significance level of P?≤?0.01 involving five SSR markers. A general linear model showed 72 marker-trait associations involving 42 SSR markers. We confirmed the presence in the general linear model associations of the five significant marker-trait associations (SMTAs) identified in the mixed linear model. For these SMTAs, two loci were associated with stem diameter and one locus each was associated with ear row number, leaf width, and leaf length. These results should prove useful for breeding new inbred lines by selecting parental lines using molecular markers and will help to preserve maize genetic resources in Korea.     

Selection of high heterozygosity popcorn varieties in Brazil based on SSR markers

We analyzed genetic structure and diversity among eight populations of popcorn, using SSR loci as genetic markers. Our objectives were to select SSR loci that could be used to estimate genetic diversity within popcorn populations, and to analyze the genetic structure of promising populations with high levels of heterozygosity that could be used in breeding programs. Fifty-seven alleles (3.7 alleles per locus) were detected; the highest effective number of alleles (4.21) and the highest gene diversity (0.763) were found for the Umc2226 locus. A very high level of population differentiation was found (F(ST) = 0.3664), with F(ST) for each locus ranging from 0.1029 (Umc1664) to 0.6010 (Umc2350). This analysis allowed us to identify SSR loci with high levels of heterozygosity and heterozygous varieties, which could be selected for production of inbred lines and for developing new cultivars.     

SSR analysis of genetic diversity among maize inbred lines adapted to cold regions of Japan

Information regarding diversity and relationships among breeding material is necessary for hybrid maize (Zea mays L.) breeding. Simple-sequence repeat (SSR) analysis of the 60 loci distributed uniformly throughout the maize genome was carried out for 65 inbred lines adapted to cold regions of Japan in order to assess genetic diversity among the inbred lines and to assign them to heterotic groups. The mean value (0.69) of the polymorphic-index content (PIC) for the SSR loci provided sufficient discrimination-ability for the assessment of genetic diversity among the inbred lines. The correlation between the genetic-similarity (GS) estimates and the coancestry coefficient was significant (r = 0.70). The average-linkage (UPGMA) cluster analysis and principal-coordinate analysis (PCOA) for a matrix of the GS estimates showed that the Northern flint inbred lines bred in Japan were similar to a Canadian Northern flint inbred line CO12 and a European flint inbred line F283, and that dent inbred lines bred in Japan were similar to BSSS inbred lines such as B73. These associations correspond to the known pedigree records of these inbred lines. The results indicate that SSR analysis is effective for the assessment of genetic diversity among maize inbred lines and for the assignment of inbred lines to heterotic groups.     

Microsatellite marker-based genetic diversity assessment among exotic and native maize inbred lines of Bangladesh

Hybrid development is basically dependent on the variability among available genetic resources. Polymorphism among the maize inbreds is essentially needed for maize hybridization. This study aimed at the assessment of diversity among 22 maize inbreds by 18 microsatellite markers. The study identified 187 alleles at 18 SSR loci. The amplified allele frequency per microsatellite locus was 10.4 and the highest allele per locus was 17 in SSR primer pair phi026. SSR primer set p-umc1292, phi074 and phi090 showed the lowest 6 alleles per genotype per locus. The locus phi026 showed the highest degree of gene diversity (0.92), and the locus p-umc1292 had the lowest of gene diversity (0.77) with a mean value of 0.862 among the microsatellites. At each site, the most prevalent allele varied between 0.14 (bnlg371) and 0.36. (p-umc1292). At any given locus, an average of 0.22 out of the 22 selected maize inbred lines had a common major allele. The average value of the polymorphic information content (PIC) was 0.85, within the range of 0.74 at the lowest to 0.92 at the highest. The higher PIC values of phi026 and nc013 established them to be the best markers for maize inbred lines. The UPGMA clustering generated seven distinct groups having 12.5% of similarity coefficient. The results revealed that inbred lines E10, E27, E19, E34, E35, E4, E43, E28, E11, E21, E17, E38, E25, E34, E14, E16, E39 and E3 were more diversified. These lines are promising to be used as parent materials for hybrid maize development in the future.     

Molecular marker-based genetic diversity assessment of Striga-resistant maize inbred lines

Striga-resistant maize inbred lines are of interest to maize breeding programs in the savannas of Africa where the parasitic weed is endemic and causes severe yield losses in tropical maize. Assessment of the genetic diversity of such inbred lines is useful for their systematic and efficient use in a breeding program. Diversity analysis of 41 Striga-resistant maize inbred lines was conducted using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers to examine the genetic relationships among these lines and to determine the level of genetic diversity that exists within and between their source populations. The two marker systems generated 262 and 101 polymorphic fragments, respectively. Genetic similarity (GS) values among all possible pairs of inbred lines varied from 0.45 to 0.95, with a mean of 0.61±0.002 for AFLPs, and from 0.21 to 0.92, with a mean of 0.48±0.003, for SSRs. The inbred lines from each source population exhibited a broad range of GS values with the two types of markers. Both AFLPs and SSRs revealed similar levels of within population genetic variation for all source populations. Cluster and principal component analysis of GS estimates with the two markers revealed clear differentiation of the Striga-resistant inbred lines into groups according to their source populations. There was clear separation between early- and late-maturing Striga-resistant inbred lines. Considering the paucity of germplasm with good levels of resistance to Striga in maize, the broad genetic diversity detected within and among source populations demonstrates the genetic potential that exists to improve maize for resistance to Striga.     

贵州70份玉米自交系的SSR标记遗传多样性及其杂种优势群分析

从251个SSR标记中筛选出均匀分布在玉米基因组上的88个SSR标记,用以分析评价贵州省2000年以来47个审定品种的70份亲本材料的遗传多样性。SSR标记检测的结果:88个标记共检测出466个等位基因,每个标记可检测等位基因2～18个,平均为5.31个;每个标记位点的多态性信息量(PIC)变化为0.213～0.965,平均为0.586,这表明贵州玉米自交系具有较为丰富的遗传多样性。POPTREE聚类分析结果:70份自交系分为Ⅰ、Ⅱ和Ⅲ类群。Ⅰ类群含8个自交系,以瑞德和兰卡斯特等温带种质为主。Ⅱ类群有11个自交系,以PN78599、瑞德和兰卡斯特等温带种质为主。Ⅲ类群拥有51个自交系,可分为A和B 2个亚群,B亚群还可再分为B1和B2 2个次亚群,A亚群中的10个系以我国地方温带种质为主,B1次亚群中的19个系以贵州地方亚热带种质为主,B2次亚群中的22个系以泰国苏湾热带种质为主。杂种优势利用分析的结果表明,贵州近些年在玉米育种中,主要是利用贵州地方亚热带种质和泰国苏湾热带种质2个杂种优势群,这与其多态位点百分率较高有关,与其群内SSR位点的平均等位数较多有关。贵州玉米育种利用的种质类型较少,有必要加强玉米种...     

Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.     

Analysis of genetic distance by SSR in waxy maize

We examined the genetic diversity of 80 inbred waxy maize lines using 22 SSR molecular markers that could be used to achieve heterosis in waxy maize. Eighty inbred waxy maize lines with different phenotypes, 40 yellow, 25 white, 13 black, and two red lines were analyzed by SSR molecular marker fingerprint and cluster analysis. Using a standard genetic distance of 0.55, the 80 waxy maize inbred lines were clustered into nine groups. Among them, group II, group V, groups VII and VIII, and group IX were divided into three subgroups at a genetic distance of 0.46, into two subgroups at 0.49, into two subgroups at 0.46, and into four subgroups at 0.493, respectively. All but one of the yellow waxy maize inbred lines were clustered in groups VI, VII, VIII, and IX. Group IX (30 lines) contained 28 yellow lines; the other 11 yellow lines were distributed among groups VI, VII and VIII. Among the 25 white lines, 21 were clustered in groups III, V, VI and the third subgroup of group II. The black line N72 was in a group of its own. The black lines N75, N76 and N78 were distributed in groups VII, VIII and IX, respectively. The other nine black lines were clustered in group II. The red lines were distributed in the second subgroup of group II and there was no difference in genetic distance between them. In conclusion, there were considerable genetic differences among waxy maize inbred lines of different colors. The mean genetic distance of inbred lines of the same color was significantly less than that of lines of different colors. Therefore, we concluded that it was more accurate to determine the difference between the populations using the highly stable DNA genetic markers.     

Tropical maize germplasm: what can we say about its genetic diversity in the light of molecular markers?

Knowledge about genetic variability of a crop allows for more efficient and effective use of resources in plant improvement programs. The genetic variation within temperate maize has been studied extensively, but the levels and patterns of diversity in tropical maize are still not well understood. Brazilian maize germplasm represents a very important pool of genetic diversity due to many past introductions of exotic material. To improve our knowledge of the genetic diversity in tropical maize inbred lines, we fingerprinted 85 lines with 569 AFLP bands and 50 microsatellite loci. These markers revealed substantial variability among lines, with high rates of polymorphism. Cluster analysis was used to identify groups of related lines. Well-defined groups were not observed, indicating that the tropical maize studied is not as well organized as temperate maize. Three types of genetic distance measurements were applied (Jaccard’s coefficient, Modified Rogers’ distance and molecular coefficient of coancestry), and the values obtained with all of them indicated that the genetic similarities were small among the lines. The different coefficients did not substantially affect the results of cluster analysis, but marker types had a large effect on genetic similarity estimates. Regardless of genetic similarity coefficient used, estimates based on AFLPs were poorly correlated with those based on SSRs. Analyses using AFLP and SSR data together do not seem to be the most efficient manner of assessing variability in highly diverse materials because the result was similar to using AFLPs alone. It was seen that molecular markers can help to organize the genetic variability and expose useful diversity for breeding purposes.     

Analyses of genetic diversity among maize inbred lines differing for resistance to pink borer and post-flowering stalk rot

Identification of the diverse sources of resistance is an important issue among the breeders for developing pest and disease free hybrids, to reduce the inoculum load, to prolong the life of inbred lines/hybrids and to reduce the cost of cultivation. Molecular diversity analysis was carried out among 23 maize inbred lines with respect to post flowering stalk rot and pink borer. Forty six SSR markers were employed among eight post flowering stalk rot (PFSR) and seven pink borer resistant lines along with eight other inbred lines to identify diverse resistant sources for developing resistant heterotic combinations to above pests and diseases. Number of alleles per SSR marker ranged from 2 to 9 averaging 4.11. The polymorphism information content (PIC) ranged from 0.272 to 0.839 with an average of 0.568. Discrimination rate (DR) of the markers ranged from 0.095 to 0.861 with a mean of 0.618. Number of alleles was highly correlated with PIC and DR. The pair-wise genetic dissimilarity values ranged from 0.05 to 0.84 with an overall mean of 0.64. Un-weighted neighbour joining clustering put 23 genotypes in two main clusters, which were further subdivided into 5 and 6 sub-clusters, respectively. We obtained 56 rare and 26 unique alleles in specific inbred lines, which can be used for identification of these lines. The present study has revealed considerable diversity among inbred lines differing for resistance against PFSR and pink borer; and provided ample scope for selection of parents for utilization in heterosis breeding     

Association analysis and population structure of flowering-related traits in super sweet corn inbred lines with simple sequence repeat markers

This study assessed the genetic and phenotypic variation of 90 super sweet corn inbred lines and performed association analyses of six agronomical traits using 100 simple sequence repeats (SSR), ultimately detecting 590 alleles, with an average of 5.90 alleles per locus. The average genetic diversity and Polymorphism information content values were 0.54 and 0.50, respectively. Using population structure analysis, inbred lines were divided into three major groups and one admixed group. Association analysis was performed with a general linear model using a Q-matrix (Q GLM) and a mixed linear model using Q and K-matrices (Q + K MLM). Q GLM found 33 marker-trait associations involving 20 SSR markers that were associated with six agronomic traits. Q + K MLM identified four marker-trait associations involving three markers that were associated with traits of days of tasseling (DT) and days of silking (DS). Q GLM and Q + K MLM detected four significant marker-trait associations (SMTAs), with a level of significance of P < 0.01. In overlapping SMTAs, phi051 was associated with DT, umc1708 was associated with DS, and umc2341 was associated with two traits: DT and DS. The detection of loci associated with traits in this study may provide greater opportunities to improve quality by marker-assisted selection (MAS). Finally, these results will be helpful for breeders in choosing parental lines for crossing combinations as well as markers for using MAS in super sweet corn breeding programs in Korea.     

Relationships among maize inbred lines and populations from European and North-American origins as estimated using RFLP markers

RFLP markers have proven to be a reliable and highly informative tool for characterizing genetic diversity in maize. Joint analysis of inbred lines and populations should provide valuable information with respect to (1) a better understanding of the genetic basis of present elite germplasm and (2) the identification of populations that may prove to be useful sources of genetic diversity for breeding programs. Sixty-two inbred lines of known heterotic groups and ten maize populations, some of them significant contributors to the genetic basis of the heterotic groups, were assayed at 28 RFLP loci. Joint data analyses first underlined that the populations displayed a large number of alleles that were absent in the set of inbred lines. Associations among inbreds and populations further proved consistent with pedigree data of the inbreds and provided new information on the genetical basis of heterotic groups. In particular, European flint inbreds were revealed to be as close to the Northeastern U.S. flint population studied as to the typical European populations. These results advocate the analysis of larger sets of populations by means of molecular markers in order to (1) gain insight into the history of maize germplasm and (2) set up appropriate strategies for the use of genetic resources in breeding programs. Received: 23 February 1998 / Accepted: 5 February 1999     

Grouping of tropical mid-altitude maize inbred lines on the basis of yield data and molecular markers

The classification of maize inbred lines into heterotic groups is an important undertaking in hybrid breeding. The objectives of our research were to: (1) separate selected tropical mid-altitude maize inbred lines into heterotic groups based on grain yield data; (2) assess the genetic relationships among these inbred lines using amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers; (3) examine the consistency between yield-based and marker-based groupings of the inbred lines. Thirty-eight tropical mid-altitude maize inbred lines were crossed to two inbred line testers representing the flint and dent heterotic pattern, respectively. The resulting testcrosses were evaluated in a trial at three locations for 2 years. Significant general combining ability (GCA) and specific combining ability (SCA) effects for grain yield were detected among the inbred lines. The tester inbred lines classified 23 of the 38 tested inbred lines into two heterotic groups based on SCA effects and testcross mean grain yields. This grouping was not related to endosperm type of the inbred lines. The outstanding performance of testcrosses of the remaining 15 inbred lines indicates the presence of significant genetic diversity that may allow the assignment of the lines into more than two heterotic groups. Diversity analysis of the 40 maize inbred lines using AFLP and SSR markers found high levels of genetic diversity among these lines and subdivided them into two main groups with subdivision into sub-groups consistent with breeding history, origin and parentage of the lines. However, heterotic groups formed using yield-based combining ability were different from the groups established on the basis of molecular markers. Considering the diversity of the genetic backgrounds of the mid-altitude inbred lines, the marker-based grouping may serve as the basis to design and carry out combining ability studies in the field to establish clearly defined heterotic groups with a greater genetic similarity within groups.Communicated by H.H. Geiger     

Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004

Analysis of genetic diversity changes in existing gene pools of cultivated crops is important for understanding the impact of plant breeding on crop genetic diversity and developing effective indicators for genetic diversity of cultivated plants. The objective of this study was to assess genetic diversity changes in 75 Canadian hard red wheat (Triticum aestivum L.) cultivars released from 1845 to 2004 using 31 simple sequence repeats (SSRs) markers. A total of 267 SSR alleles were detected, and their allelic frequencies ranged from 0.01 to 0.97, with an average of 0.14. Significant allelic reduction was observed at only four SSR loci for the cultivars released from 1970 onwards. However, 51 alleles (about 19%) present in pre-1910 cultivars were undetected in cultivars released after 1990 and were spread over 27 SSR loci. The proportion of SSR variation accounted for by six breeding periods was 12.5%, by four ancestral families, 16.5%, and by eight breeding programs, 8.4%. The average genetic diversity measured by three different band-sharing methods did not change significantly among cultivars released from different breeding periods, breeding programs, and ancestral families. However, genetic shift was obvious in the cultivars released over the six breeding periods, reflecting well the various breeding efforts over years. These results clearly show the allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released over time. Consequently, more effort needs to be made to broaden the wheat breeding base and conserve wheat germplasm.     

The use of SSRs for predicting the hybrid yield and yield heterosis in 15 key inbred lines of Chinese maize

A challenge to maize breeders is to predict and identify inbred lines that can produce highly heterotic hybrids precisely. In the present study we surveyed the genetic diversity among 15 elite inbred lines of maize in China with SSR markers and assessed the relationship between SSR marker and hybrid yield/yield heterosis in a diallel set of 105 crosses. Forty-three SSR primers selected from all sixty-three primers gave stable profiles amplified in the sample of 15 inbred lines, which could clearly resolve on 4% metaphor agarose gel. The average number of alleles per SSR locus was 4.44 with a range from 2 to 9. The polymorphism information content (PIC) for the SSR loci varied from 0.28 to 0.81 with a mean of 0.6281. Genetic similarity (GS) among 15 lines was estimated with 191 alleles identified as raw data, the Nei's coefficient of GS ranged from 0.492 for 478 vs HZ4 up to 0.745 for E28 to ZH64 with a mean of 0.619. The cluster diagram based upon the SSR data grouped the 15 lines into families consistent with the yield heterotic response of these. Genetic distance (GD) based on SSR data was significantly correlated with hybrid yield/yield heterosis, the correlation coefficient (r) being 0.5432 and 0.4271 in 1999 and 0.4305 and 0.3614 in 1998 field test, respectively, whereas the determination coefficient (r2) was lower. The correlation between GD based on SSR data and hybrid yield/yield heterosis changed alone with the difference of number and pedigree relationship among parents that were used in this study. SSR makers showed high polymorphism and could be used to assess the relationship between inbred lines of maize, but it was difficult to predict the yield heterosis of maize.     

Linkage disequilibrium in European elite maize germplasm investigated with SSRs

Information about the extent and genomic distribution of linkage disequilibrium (LD) is of fundamental importance for association mapping. The main objectives of this study were to (1) investigate genetic diversity within germplasm groups of elite European maize (Zea mays L.) inbred lines, (2) examine the population structure of elite European maize germplasm, and (3) determine the extent and genomic distribution of LD between pairs of simple sequence repeat (SSR) markers. We examined genetic diversity and LD in a cross section of European and US elite breeding material comprising 147 inbred lines genotyped with 100 SSR markers. For gene diversity within each group, significant (P<0.05) differences existed among the groups. The LD was significant (P<0.05) for 49% of the SSR marker pairs in the 80 flint lines and for 56% of the SSR marker pairs in the 57 dent lines. The ratio of linked to unlinked loci in LD was 1.1 for both germplasm groups. The high incidence of LD suggests that the extent of LD between SSR markers should allow the detection of marker-phenotype associations in a genome scan. However, our results also indicate that a high proportion of the observed LD is generated by forces, such as relatedness, population stratification, and genetic drift, which cause a high risk of detecting false positives in association mapping.     

Study of genetic diversity and relationships among accessions of foxtail millet [Setaria italica (L.) P. Beauv.] in Korea, China, and Pakistan using SSR markers

In this study, 28 simple sequence repeat (SSR) primer sets were used to analyze the genetic diversity, population structure, and genetic relationships among 37 accessions of foxtail millet from Korea, China and Pakistan. A total of 298 alleles were detected with an average allele number of 10.6 per locus among 37 foxtail millet accessions. The number of alleles per locus ranged from 2 (b226) to 20 (b236). Of the 298 alleles, 138 alleles (46.3%) were rare (frequency < 0.05), 152 alleles (51.0%) were detected at an intermediate frequency (range, 0.05?C0.50), and eight alleles (2.7%) were abundant (frequency > 0.50), respectively. The average gene diversity values were 0.652, 0.692, and 0.491 and polymorphic information content values were 0.621, 0.653, and 0.438, for accessions from Korea, China, and Pakistan, respectively. The accessions from China showed higher SSR diversity than those from Korea and Pakistan. A phylogenetic tree constructed using the un-weighted pair group methods with arithmetic mean algorithm revealed three major groups of accessions that were not congruent with geographical distribution patterns with a few exceptions. The lack of correlation between the accession clusters and their geographic location indicates that the diffusion of foxtail millet from China to Korea might have occurred through multiple routes. Our results provide support for the origin and diffusion route of foxtail millet in East Asia. This SSR-based assessment of genetic diversity, genetic relationships, and population structure among genetic resources of foxtail millet landraces will be valuable to foxtail millet breeding and genetic conservation programs in Korea.     

Analysis of genetic mapping in a waxy/dent maize RIL population using SSR and SNP markers

A maize genetic linkage map was generated using SSR and SNP markers in a F_7:8 recombinant inbred line (RIL) population derived from a cross of waxy corn (KW7) and dent corn (Mo17). A total of 465 markers, including 459 SSR and 6 SNP markers, were assigned to 10 linkage groups which spanned 2,656.5 cM with an average genetic distance between markers of 5.7 cM, and the number of loci per linkage group ranged from 39 to 55. The SSR (85.4%) and SNP (83.3%) markers showed Mendelian segregation ratios in the RIL population at a 5% significance threshold. In linkage analysis of six SNP loci associated with kernel starch synthesis genes (ae1, bt2, sh1, sh2, su1, and wx1), all six loci were successfully mapped and are closely linked with SSR markers in chromosomes 3 (sh2), 4 (su1 and bt2), 5 (ae1), and 9 (sh1 and wx1). The SSR markers linked with genes in starch synthesis may be utilized in marker assisted breeding programs. The resulting genetic map will be useful in dissection of quantitative traits and the identification of superior QTLs from the waxy hybrid corn. Additionally, these data support further genetic analysis and development of maize breeding programs.