The characterization and assessment of genetic diversity among maize (Zea mays L.) hybrids that are widely grown in France: Chromatographic data and isozymic data

Summary Zein chromatographic and isozyme electrophoretic data were used to characterize 61 hybrids of maize (Zea mays L.) that are of current widespread usage in France. A similar study was also carried out for 88 hybrids that are widely available in the central corn belt of the U.S. Objectives were to 1) investigate the degree to which isozyme and chromatographic data could provide unique hybrid identification; 2) to evaluate the wealth of genetic diversity available among hybrids that are currently cultivated in France and in the U.S.; and 3) to compare the patterns and extent of genetic diversity found in both countries with respect to their registration, breeding, and seed production practices.Isozyme data showed that all French hybrids were unique germplasm. However, numerous hybrids had chromatographic profiles that were identical for 11 major peaks and these hybrids could thus have some common germplasm at least among their female parental lines. Although there was a broad base of isozymic diversity among French hybrids, the amount in cultivation was less since the few most widely used hybrids, which were planted on approximately half the cultivated area, were similar for their isozymic and zein chromatographic profiles. Approximately only 50% of the U.S. hybrids were shown to be unique with the remainder classified into groups; at least some of the hybrids within each group could be genetically identical products. Leading U.S. hybrids were unique germplasm but numerous hybrids that collectively covered a large acreage appeared to encompass a relatively narrow genetic base.For the continued success of agriculture, it will be important to improve breeding, registration, and marketing practices in order to ensure the continued supply of genetically different and improved elite hybrids.     

Cluster analysis of RFLP data from related maize inbred lines of the BSSS and LSC heterotic groups and comparison with pedigree data

Summary In this study, 31 elite inbred lines of maize (Zea mays L.) were analyzed with 149 clone-enzyme combinations for their respective RFLP profiles. Objectives were (1) to determine the utility of RFLPs for estimation of genetic similarties among 16 inbred lines from the Iowa Stiff Stalk Synthetic (BSSS) and among 15 inbred lines from the Lancaster Sure Crop (LSC) heterotic groups and (2) to compare genetic similarities based on molecular markers with those based on pedigree information. Coefficients of genetic similarity (GS) and coancestry (f) between pairs of lines from the same heterotic group were calculated from RFLP and pedigree data, respectively. For lines from the BSSS heterotic group, cluster analyses based on RFLP and pedigree data revealed similar associations. GS and f values were closely correlated (r=0.70) for related BSSS lines. For lines from the LSC heterotic group, considerable discrepancies existed between the GS and f values, especially for those pairs involving inbreds Va22 and Lo924. Effect of selection and/or erroneous pedigree records are discussed as possible explanations for the low correlation of GS and f values (r=0.07) for related LSC lines. RFLPs seem useful for investigation of relationships among maize inbreds, verification of pedigree records, and quantification of the degree of relatedness.     

RFLP variation and genetic relationships in cultivated cucumber

Summary Two sets of cucumber (Cucumis sativus L.) germplasm were used to determine the potential use of restriction fragment length polymorphisms (RFLPs) for estimating genetic relationships. Sixteen accessions [15 domesticated variety sativus and one feral variety hardwickii (PI 183967)] of diverse origin were used to assess RFLP variation in cucumber, and to determine if genetic relationships based on RFLPs were similar to those obtained by isozyme analysis. Additionally, 35 commercial lines or cultivars were surveyed to determine genetic relationships among and within common cucumber types (narrow genetic base). The 16 accessions were surveyed with 440 low copy clones from two libraries (Pst I partial genomic and cDNA) using two restriction enzymes. Data from a subset of 104 random (mapped and unmapped) and a set of 30 mapped RFLPs were used to estimate genetic relationships among the 16 cultigens. Variability was low among RFLPs (33% of all probes) and putative alleles ( 2.2 polymorphic fragments/probe). RFLP variation between sativus lines and hardwickii (21±4%) was greater than among sativus lines (12±2%). RFLPs among the 16 accessions revealed genetic relationships which agree with those obtained using isozymes. Genetic relationships estimated using mapped and unmapped RFLPs were similar. The 35 elite lines were surveyed using a set of 40 RFLPs from 3 libraries (Pst I and EcoR I partial genomic and cDNA) to evaluate the discriminatory value of RFLPs among and between commercial cucumber types. The RFLP-derived genetic relationships among this germplasm were in agreement with predictions based on fruit type and pedigree information. Thus, RFLPs are a useful addition to the morphological characters and isozyme loci currently used for taxonomic classification and plant variety protection of cucumber.     

Genetic characterization of 218 elite CIMMYT maize inbred lines using RFLP markers

Characterization of genetic diversity among maize inbred lines can facilitate organization of germplasm and improve efficiency of breeding programs. A set of 218 phenotypically diverse inbred maize lines developed at CIMMYT for hybrid production was characterized using 32 RFLP markers to: (1) analyze the genetic diversity present; (2) define potential heterotic groups based on clusters formed with marker data; and (3) identify the most representative testers for each potential heterotic group. Lines were clustered using five different genetic distance measurements to find consensus non-hierarchical clusters. Dendrograms were produced to study hierarchical classification within smaller groups of lines. A very high average allelic diversity was seen in this germplasm. Lines did not cluster based on phenotype, environmental adaptation, grain color or type, maturity, or heterotic response (as determined based on hybrid performance with testers), but lines related by pedigree usually did cluster together. Previously defined testers from opposite heterotic groups were not genetically differentiated, and did not represent well their heterotic group. Discrete clusters were difficult to find; thus, potential heterotic groups will be difficult to suggest using RFLP markers alone. However, suggestions on how to use molecular markers and cross performance information to refine heterotic groups and select representative testers are presented.     

Genetic diversity of soybean germplasm resistant to Heterodera glycines

Information on the genetic background of soybean [Glycine max (L.) Merr.] germplasm resistant to Soybean Cyst Nematode (SCN) (Heterodera glycines Ichinohe) is essential for developing plant breeding strategies, however, pedigree information for SCN resistant germplasm is not always available. Using restriction fragment length polymorphisms (RFLPs) to fingerprint different soybean lines is a useful means of determining genetic relationships and identifying unique genotypes. In this study, 102 soybean genomic probes with five different restriction enzymes were used to detect DNA variations and investigate genetic relationships among 56 soybean plant introductions (PIs) and cultivars. Among 510 probe/enzyme combinations, a total of 1707 hybridization bands were generated, of which 501 were polymorphic. A cluster dendrogram and a principal component analysis (PCA) plot diagram were constructed using DNA fingerprinting of the 56 soybean lines. Based on the clustering and PCA analyses, two major clusters comprising 15 groups were identified for the PIs and cultivars in the dendrogram. Reactions to different race isolates of SCN were distinguishable among different groupings of the clusters and PCA results, and various origins of the PIs and the pedigree information of the cultivars could be associated with the different clusters. Additional information on the appropriate number of probes used to detect genetic diversity more efficiently was elucidated through this research. We believe that the genetic relationships determined among these 56 soybean lines could provide useful information in identifying unique sources of genes for SCN resistance. This revised version was published online in July 2006 with corrections to the Cover Date.     

Components of variation,heritabilities and correlations for indices of sprouting tolerance and seed dormancy in Triticum spp.

Summary RFLPs were used to study the genetic relationships of 31 Portuguese coles (Brassica oleracea L.) representing the different ecotypes or landraces grown in Portugal. Other cole crops such as Jersey kale, Chinese kales, common cabbages, broccolis and cauliflower, two nine-chromosome wild species, and one accession of turnip also were included to determine the evolutionary relationships of Portuguese coles to other related coles. Principal coordinates and cluster analyses were conducted using a package of computer programs and RFLP data from 55 nuclear DNA probes, detecting 291 polymorphic restriction fragments. The results showed that the 48 accessions clustered into five groups: (a) a dispersed group with turnip and the wild brassicas; (b) Chinese kales; (c) broccolis and cauliflower; (d) a disperse group including Algarve and Jersey kales, thousand head kale, cabbages, and savoy cabbage; (e) a large and compact group containing all Portuguese tronchuda cabbages and kales. This unique and closely related group containing Portuguese tronchuda cabbages and kales could be further divided into five subgroups corresponding to the major areas of cultivation. The phenetic groupings of Portuguese tronchuda cabbages and kales based on RFLP data corresponded more with their geographic origins (collecting sites) than with their morphological similarities. A mechanism involving geographic isolation and frequent intercrossing within local areas is proposed to explain genetic relationships among Portuguese tronchuda cabbages and kales.     

Genetic diversity of Brassica napus L. Germplasm from China and Europe assessed by some agronomically important characters

Summary The genetic diversity and relationships among 63 rapeseed accessions, including 34 Chinese, 22 Czech, 2 Swedish, 2 German, one French and 2 Canadian accessions, were evaluated by nine agronomically important characters in the field at Yangling, Shaanxi, China. Significant differences between Chinese and European group in plant height, setting position of the first primary branch, number of siliques of the terminal raceme, thousand seed weight and seed yield per plant were detected. There were significant variations in nine agronomic characters among the tested rapeseed accessions. Ward’s minimum variance cluster analysis based on Mahalanobis distances on the raw data of nine agronomic characters clearly separated the European accessions from the Chinese ones. However, the Chinese accessions with erucic acid free and/or low glucosinolates could not be separated from those Chinese accessions with both high erucic acid and glucosinolates. In general, cluster analysis of the 63 accessions based on the selected agronomic characters was consistent with known pedigree information and geographic origin, as well as the previous RAPD results of these accessions. The European rapeseed could be important germplasm resources for enriching the genetic background of Chinese rapeseed, and vice versa.     

Genetic diversity within Australian wheat breeding programs based on molecular and pedigree data

124 wheat cultivars and breeding lines were screened with 19 microsatellite (SSR) loci generating 160 scorable bands which were used to construct a genetic distance (GD) matrix. A distance matrix based on coefficient of parentage (COP) scores was also generated for the cultivars for which good pedigree records were available. The SSR and COP data for 101 of the wheat cultivars were compared with genetic distance scores obtained using1898 scorable restriction fragment length polymorphism (RFLP) bands previously generated. Phylograms were generated based on the SSR, RFLP,combined SSR and RFLP and COP data. The standardised Mantel's Z test showed that the distance matrices generated from all of the data sets were significantly correlated. Bootstrap analysis showed that, although the SSR and RFLP data were correlated, a large number of SSR loci are required for determining robust genetic relationships between large numbers of cultivars. In addition, accurate pedigree records are needed to determine genetic relatedness using COP. The molecular data were also used to determine the level of genetic variability within breeding programs and to assess the impact of the introduction of semidwarf and other germplasm. The results showed that the level of genetic diversity in Australian wheat cultivars has increased over time and that in particular, the introduction of semidwarf germplasm resulted in an increase in the overall diversity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic diversity among elite Bulgarian barley varieties evaluated by RFLP and RAPD markers

Genetic variation among five elite winter barley cultivars (H. vulgare L.) currently grown in Bulgaria was assessed at the molecular level using restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) markers. The present study sampled RFLPs in four well characterized multigene families in barley: the seed storage protein loci; the 18S, 5.8S and 26S ribosomal DNA loci; the loci coding for 5S ribosomal RNA and the loci coding subunit α of ATP-A complex in the mitochondrial genome. RFLPs were detected in three out of five investigated chromosomal loci in the barley cultivars studied. RAPD assay using arbitrary 10-base primers was applied to generate amplified length polymorphic markers in barley. Overall a total of 15 polymorphic phenotypes were found among the studied barley cultivars by using 11 out of 25 tested primers. All RAPDs were considered as dominant genetic markers except for two, where PCR and Southern blot analysis indicated the presence of codominant amplification products. Five RAPD polymorphisms in F₁ and F₂ progenies of the cross between Alpha and Obzor were inherited in Mendelian fashion. The determined values for the genetic variation proved a high genetic similarity among the tested cultivars. Genetic similarity (GS) calculated from RFLP and RAPD data ranged from 0.888 to 0.997 with a mean GS – 0.933. This revised version was published online in July 2006 with corrections to the Cover Date.     

Long-term association of locations for testing spring bread wheat

Summary The International Spring Wheat Yield Nursery (ISWYN) has been distributed annually since 1964 and the results provide a base for investigating relationships among locations. Ordination and clustering of locations was conducted using 26 years of grain yield data. Ordination and clusters based on the discrimination of germplasm were compared with mega-environments, which are groupings of locations defined by CIMMYT on the basis of climatic factors and perceptions of major biotic and abiotic stresses. Discrepancies among mega-environmental groupings, clusters and ordinations may identify locations for which major stresses affecting wheat yield are yet unidentified.Major environmental discriminators were latitude and the presence or absence of stress, although there was little association of locations due to limited moisture availability. We identified two major spring wheat environments, typified as Asian and European, and suggest the mega-environmental classification does not explain all significant associations among locations. Location groupings based on discrimination of germplasm should be considered in parallel to mega-environments on a regular basis and we propose breeding for a base of broadly adapted germplasm to which specific stress tolerances are incorporated.Abbreviations CIMMYT International Maize & Wheat Improvement Centre - ISWYN International Spring Wheat Yield Nursery - WANA West Asia and North Africa     

Genetic diversity of barley cultivars grown in Spain, estimated by RFLP, similarity and coancestry coefficients

This study was conducted with the objective of characterizing the genetic variation among a representative set of 37 barley cultivars currently grown in Spain, using restriction fragment length polymorphism (RFLP) markers. Thirty-two RFLP probes, in combination with three restriction enzymes, were used to analyse polymorphism at the molecular level. Genetic distances (GD), based on RFLP band patterns, and coancestry coefficients (f), based on pedigree records, were calculated. Of the 95 clone-enzyme combinations analysed, 71 (74.7%) were polymorphic, representing 246 RFLP patterns. A cluster analysis of GD split the sample into five distinct germplasm groups that were consistent with the history of the cultivars (winter European, spring European, CIMMYT-ICARDA materials, the single cultivar ‘Dobla’ and Spanish local materials). The Spanish group was the most distinct one and had unique alleles at markers close to major loci determining phonological adaptation. The probes which best distinguished among groups were also identified. Genetic similarity estimates were moderately consistent with f (for cultivars with complete pedigrees). The implications for integration of diversity studies into breeding programmes are discussed.     

Patterns of RFLP-based genetic diversity in germplasm pools of common wheat with different geographical or breeding program origins

A set of 292 accessions of common wheat (Triticum aestivum L.) representing 21 germplasm pools based on geographical or breeding program origins was assayed for RFLP diversity. Thirty cDNA and genomic DNA probes and the HindIII restriction enzyme were employed for RFLP analysis. About 61% of all 233 scored bands were present in 75% or more of the accessions. All but one of the 30 probes revealed polymorphism, and the average number of distinct patterns per probe over all accessions was 9.5.Polymorphic Information Content (PIC) values within a pool varied from 0 to 0.9 and depended on the identities of both the germplasm pool and the probe. Rare banding patterns with a relative frequency of ≤0.2 within a pool were detected. These rare patterns were more likely to occur in pools exhibiting high levels of heterogeneity. The highest level of polymorphism was observed in the Turkish landraces from Southwest Asia. The Eastern U.S. soft red winter wheat germplasm pool was more genetically diverse than the other advanced germplasm pools, and nearly as diverse as the Turkish landrace pool. RFLP-based genetic relationships between germplasm pools generally tracked expectations based on common geographical origin, breeding history and/or shared parentages. The Chinese wheat landraces from Sichuan, Tibet, and Yunnan provinces were distinct from other pools. Similarity matrices for among-pool genetic distance estimates based on either band frequencies or banding pattern frequencies showed good correlation with matrices derived from Nei and Li's mean genetic similarity estimates (r=−0.82^** and r=−0.73^**, respectively. This revised version was published online in July 2006 with corrections to the Cover Date.     

RFLP characterization of Indian Musa germplasm for clonal identification and classification

Summary Nineteen single-copy clones isolated from a PstI genomic library (cv. Maiden Plantain), and eight Vigna chloroplast DNA clones were used to probe total genomic DNA digests of 57 genotypes of Musa from India. The 19 genomic clones detected a total of 107 polymorphisms among the 57 genotypes. Principal coordinates and phenetic analyses of these data placed cultivars and species into distinct groups that were in general agreement with a previously published RAPD-based classification of these same plant materials. The 107 polymorphisms were sufficient to differentiate each clone from every other clone. Heterologous Vigna chloroplast DNA probes were used to characterize the cytoplasm of Musa cultivars and species. PCO analysis of these RFLPs were detected both within and between the generally recognized genome groups, indicating multiple hybridization pathways in the origin of hybrid clones. Data presented demonstrate that RFLPs are sufficiently abundant to classify Musa germplasm and that genetic relationships among Musa cultivars, based upon RFLP data, are in general agreement with relationships determined by analysis of morphology and RAPDs.     

ISSR Analysis of Genetic Background of Triploid Female and Diploid Male of Siraitia grosvenorii

[Objective] To evaluate the genetic background of triploid female and diploid male of Siraitia grosvenorii and to provide biological references for fine varieties breeding of seedless S. grosvenorii. [Methods]Inter simple sequence repeats(ISSR) marker was developed to analyze the genetic background among 28 samples of S. grosvenorii,and cluster analysis and double principal coordinate analysis were revealed by the NTSYS-pc software and Gen AIEx software,respectively. [Results]13 ISSR primers selected out of 100 primers for amplification,and a total of 131 unambiguous bands were obtained,among which 99(PPB = 75. 57%) were polymorphic. The results of cluster analysis and double principal coordinate analysis showed that there was a certain richness of genetic background in triploid female and diploid male of S. grosvenorii. But the genetic similarity coefficients of majority were relatively great with close genetic distance. [Conclusions] The triploid female and diploid male of S. grosvenorii had relatively low complexity of genetic background,so that germplasm innovation strategies should be carried out to enrich the genetic background of seedless S. grosvenorii.     

Molecular mapping of a new gene for resistance to rice blast (Pyricularia grisea Sacc.)

A single dominant blast resistance gene conferring resistance to a Korean rice blast isolate was identified in rice variety `Suweon 365'. We report the chromosomal localization and molecular mapping of this blast resistance gene designated as Pi-18, which confers resistance to Korean isolate `KI-313' of the blast pathogen. To know whether there is a relationship among genes conditioning resistance to location-specific isolates of the blast pathogen and thereby to identify linked markers to resistance gene for isolate KI-313 collected in Korea, RFLP markers previously reported to be linked to major blast resistance genes in different rice germplasm and other markers mapped to nearby regions were surveyed for polymorphism between a resistant (`Suweon 365') and a susceptible (`Chucheongbyeo') parent. Linkage associations of the RFLP markers with the resistance gene were verified using an F2 and F3 segregating population of known blast reaction. RFLP analysis showed that Pi-18 was located near the end of chromosome 11, linked to a single copy clone RZ536 at a distance of 5.4 centiMorgans (cM) and that this gene was different from Pi-1(t). An allelism test revealed that this gene was also different from Pi-k. Currently, a combination of RAPD and microsatellite primers is being employed to find additional markers in this region. Tightly linked DNA markers will facilitate selection for resistant genotypes in breeding programs and provide the basis for map based cloning of this new blast resistance gene. This revised version was published online in July 2006 with corrections to the Cover Date.     

Relationship between heterosis and genetic divergence in 'Tongil'-type rice

Improving grain yield and quality of ‘Tongil’‐type rice (indica/japonica) continues to be a major breeding objective in Korea. In this study, genetic divergence among 13‘Tongil’‐type rice cultivars was evaluated and the relationship between genetic distance and hybrid performance in all possible nonreciprocal crosses between them assessed. The 78 F₁ hybrids together with the 13 parents were evaluated for eight traits of agronomic importance, including yield, in a replicated field trial. The 13 parents were examined for DNA polymorphism using 71 micro‐satellite or simple sequence repeats and 46 random decamer oligonucleotide primers. A total of 319 polymorphic variants were generated and, based on the polymorphism data, genetic distances (GDs) ranged from 0.021 to 0.437. Cluster analysis based on GDs revealed associations among cultivars which was in agreement with the pedigree data. Heterosis was observed in hybrids for most of the traits, and yield exhibited the highest heterosis among the eight traits examined. The correlation values of GDs with F₁ performance were mostly nonsignificant, except for yield, culm length and spikelets per panicle. The correlations of GDs with midparent and better‐parent heterosis were not significant enough to be of predictive value. These results indicate that GDs based on the microsatellite and random amplified polymorphic DNA (RAPD) markers may not be useful for predicting heterotic combinations in ‘Tongil’‐type rice and support the idea that the level of correlation between hybrid performance and genetic divergence is dependent on the germplasm used.     

Molecular stability of the ribosomal RNA genes in Solanum tuberosum plants recovered from slow growth and cryopreservation

Summary Ribosomal gene (rDNA) probes have been used to assess genomic changes in plants of (1) S. tuberosum cv Desiree subjected to slow growth and (2) S. tuberosum cv Golden Wonder recovered from cryopreservation. Restriction fragment length polymorphisms (RFLPs) were detected in two out of 16 DNA samples extracted from plants derived from slow growth, control plants did not show RFLP differences. Plants recovered from cryopreserved shoot-tips of Golden Wonder were unchanged in their ribosomal gene RFLP profile compared to the untreated controls. The use of rDNA probes as tools to assess stability, and the possible detrimental effects of slow growth, somaclonal variation, cryoprotectants, and freezing injury are discussed.     

Linkage groups of isozymes,RFLP and RAPD markers in carrot (Daucus carota L. sativus)

Summary Genetic and linkage analysis of marker loci were performed with 4 selfed progenies, derived from single plant (I_0/1 lines) of carrot (Daucus carota L. sativus). The analysis of 58 markers included 1 morphological marker, 10 isozyme loci, 14 RFLPs, 28 RAPD markers, and 6 isolated PCR fragments used as RFLP probes. Linkage analysis was carried out with the MAPMAKER program and resulted in the construction of 8 linkage groups containing 55 markers with an average distance of 13.1 cM, 3 marker loci remained unlinked. 24% of the markers deviated significantly from the expected Mendelian ratios (1:2:1 or 3:1) due to gametic or zygotic selection. It was shown that isolated PCR amplification products can be used as RFLP probes to detect polymorphisms for a certain locus in progenies where the corresponding RAPD pattern is monomorphic or no amplification product is observed. Since carrot has a relative small genome the probability of amplifying repetitive DNA sequences is comparatively low. Thus PCR amplification products represent an additional useful source of RFLP probes.     

Assessing the genetic diversity of Portuguese maize germplasm using microsatellite markers

A collection of Portuguese maize accessions representing a valuable source of genes for introduction into modern cultivars is stored at the Portuguese Plant Germplasm Bank (Banco Português de Germoplasma Vegetal—BPGV). To assess genetic diversity among inbreds, microsatellite analysis was carried out for 54 inbred lines representing the diversity of Portuguese dent and flint maize germplasm. Fifty American and other European elite inbreds were also analysed for comparison. Fifteen microsatellite loci distributed throughout the maize genome were chosen based on their repeat unit and base composition. A total of 80 alleles were detected with an average allele number of 5.33 per locus. Polymorphism information content (PIC) values and observed genetic distances showed the existence of large variability among inbreds. Cluster analysis indicated that almost all of the inbreds could be distinguished from each other and Portuguese inbreds were present in all clusters formed. These associations were consistent with the known pedigree records of the inbreds, confirming a mixed origin of Portuguese materials. Comparative analysis of microsatellite diversity among groups was established according to important traits for both breeding and line identification. This revealed that, although most of the genetic diversity (>95%) was attributable to differences among inbreds of different groups, the existence of phenotypic differentiation in endosperm colour, kernel type and cob colour could be suggested for grouping. These findings support the joint use of molecular and morphological traits in management of the germplasm collection. In this study, SSR markers proved to be effective to characterise and identify maize inbred lines, and demonstrate associations among them. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic distance among doubled haploid maize lines and their testcross performance under drought stress and non-stress conditions

In contrast to conventional inbreeding that takes up to seven generations to develop inbred lines, the doubled haploid (DH) technology allows production of inbred lines in two generations. The objectives of the present study were to: (a) evaluate testcross performance of 45 doubled haploid lines under drought stress and non-stress conditions (b) estimate heritabilities for grain yield and other traits and (c) to assess the genetic distance and relationship among the DH lines using 163,080 SNPs generated using genotyping-by-sequencing (GBS). The 45 hybrid and five checks were evaluated using a 10 × 5 alpha lattice in six drought stress and nine well-watered environments in Kenya, Uganda, and Tanzania. Differences in trait means between the drought stress and well-watered conditions were significant for all measured traits except for anthesis date. Genetic variances for grain yield, grain moisture, plant height and ear height were high under well-watered environments while genetic variance for anthesis date, root lodging and stalk lodging were high under drought stress environments. Combined analyses across drought stress and well-watered environments showed that ten top hybrids produced 1.6–2.2 t/ha grain yield under well-watered condition and 1–1.4 t/ha under drought stress condition higher than the mean of the commercial checks. Genetic distance between pairwise comparisons of the 38 of the 45 DH lines ranged from 0.07 to 0.48, and the overall average distance was 0.36. Both cluster and principal coordinate analysis using the genetic distance matrix calculated from 163,080 SNPs showed two major groups and the patterns of group was in agreement with their pedigree. Thirteen (13) of the best hybrids are currently in National Performance Trials testing, an important step towards commercialization in Kenya, Tanzania and Uganda.