scholarly journals SNP-based assessment of genetic purity and diversity in maize hybrid breeding

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0249505
Author(s):  
Chimwemwe Josia ◽  
Kingstone Mashingaidze ◽  
Assefa B. Amelework ◽  
Aleck Kondwakwenda ◽  
Cousin Musvosvi ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Inbred Lines ◽  
Genetic Distances ◽  
Snp Markers ◽  
Hybrid Breeding ◽  
Maize Breeding ◽  
Genetic Purity ◽  
Maize Hybrid ◽  
Dh Lines ◽  
High Level

Assessment of genetic purity of parental inbred lines and their resultant F1 hybrids is an essential quality control check in maize hybrid breeding, variety release and seed production. In this study, genetic purity, parent-offspring relationship and diversity among the inbred lines were assessed using 92 single-nucleotide polymorphism (SNP) markers. A total of 188 maize genotypes, comprising of 26 inbred lines, four doubled haploid (DH) lines and 158 single-cross maize hybrids were investigated in this study using Kompetitive Allele Specific Polymerase Chain Reaction (KASP) genotyping assays. The bi-allelic data was analyzed for genetic purity and diversity parameters using GenAlex software. The SNP markers were highly polymorphic and 90% had polymorphic information content (PIC) values of > 0.3. Pairwise genetic distances among the lines ranged from 0.05 to 0.56, indicating a high level of dissimilarity among the inbred lines. A maximum genetic distance of (0.56) was observed between inbred lines CKDHL0089 and CML443 while the lowest (0.05) was between I-42 and I-40. The majority (67%) of the inbred lines studied were genetically pure with residual heterozygosity of <5%, while only 33% had heterozygosity levels of >5%. Inbred lines, which were not pure, require purification through further inbreeding. Cluster analysis partitioned the lines into three distinct genetic clusters with the potential to contribute new beneficial alleles to the maize breeding program. Out of the 68 hybrids (43%) that passed the parent-offspring test, seven hybrids namely; SCHP29, SCHP95, SCHP94, SCHP134, SCHP44, SCHP114 and SCHP126, were selected as potential candidates for further evaluation and release due to their outstanding yield performance.

scholarly journals SNP- Based Assessment of Genetic Purity and Diversity in Maize Hybrid Breeding

2021 ◽  
Author(s):  
Chimwemwe Josia ◽  
Kingstone Mashingaidze ◽  
Assefa B. Amelework ◽  
Aleck Kondwakwenda ◽  
Cousin Musvosvi ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Inbred Lines ◽  
Genetic Distances ◽  
Snp Markers ◽  
Hybrid Breeding ◽  
Maize Breeding ◽  
Genetic Purity ◽  
Maize Hybrid ◽  
Dh Lines ◽  
High Level

AbstractAssessment of genetic purity of inbred lines and their resultant F1 hybrids is an essential quality control check in maize hybrid breeding, variety release and seed production. In this study, genetic purity, parent-offspring relationship and diversity among the inbred lines were assessed using 92 single-nucleotide polymorphism (SNP) markers. A total of 188 maize genotypes, comprising of 26 inbred lines, four doubled haploid (DH) lines and 158 single-cross maize hybrids were investigated in this study using Kompetitive Allele Specific Polymerase Chain Reaction (KASP) genotyping assays. The bi-allelic data was analyzed for genetic purity and diversity parameters using GenAlex software. The SNP markers were highly polymorphic and 90% had polymorphic information content (PIC) values of > 0.3. Pairwise genetic distances among the lines ranged from 0.05 to 0.56, indicating a high level of dissimilarity among the inbred lines. Maximum genetic distance of (0.56) was observed for CKDHL0089, CML443 and CB323, while the lowest (0.05) was between I-42 and I-40. The majority (67%) of the inbred lines studied were genetically pure with residual heterozygosity of <5%, while only 33% were had heterozygosity levels of >5%. Inbred lines, which were not pure, require purification through further inbreeding. Cluster analysis partitioned the lines into three distinct genetic clusters with the potential to contribute new beneficial alleles to the maize breeding program. Out of the 68 hybrids (43%) that passed the parent-offspring test, seven hybrids namely; SCHP29, SCHP95, SCHP94, SCHP134, SCHP44, SCHP114 and SCHP126, were selected as potential candidates for further evaluation and release due to their outstanding yield performance.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

scholarly journals Combining ability and response to CMS in reverse diploid maize lines developed at VIR

2020 ◽  
Vol 2 (4) ◽  
pp. 15-23
Author(s):  
E. B. Khatefov ◽  
B. R. Shomakhov ◽  
R. S. Kushkhova ◽  
R. A. Kudaev ◽  
Z. T. Khashirova ◽  
...  
Keyword(s):  
Combining Ability ◽  
Selection Index ◽  
Inbred Lines ◽  
Breeding Value ◽  
Hybrid Breeding ◽  
Maize Breeding ◽  
Tetraploid Population ◽  
Grain Moisture ◽  
Hybrid Maize ◽  
Period Duration

Abstract. Hybrid maize breeding requires constant renewal of the source material. In this regard, broadening of genetic variation in parental lines is one of the primary tasks in heterotic hybrid breeding programs. The use of reverse diploid inbred lines derived from a tetraploid population is considered as an innovative approach to achieve this goal.Results. The investigated material comprised 106 reverse diploid (rediploid) inbred lines originating from diploid plants selected in segregating selfed progenies of triploid populations and consequently subjected to inbreeding, while triploid populations resulted from a cross between plants of a tetraploid population with a broad genetic basis and a diploid line. The use of a system of crosses with 37 sterile testers belonging to different FAO maize maturity groups allowed the evaluation of the rediploid lines’ combining ability and the response to M and C types of CMS. Field tests were conducted in 2019 in the steppe zone of Kabardino-Balkaria. Forty-six lines (43.3%) with the combining ability ranging from ultra-high to good, and 78 lines (73.6%) maintaining the CMS character were identified. Among them, 59 lines (55.7%) were maintainers for the M type CMS, 15 lines (14.1%)  for C type CMS, and 4 lines maintained sterility for both CMS types. Sixteen lines (15.1%) restored pollen fertility of the forms with M type CMS, 11 lines (10.4%) were restorers for the C-type and one line turned out to be a universal restorer for both CMS types. Ranking by the “sprout - flowering of ears” interstage period duration showed that most of the lines (66.0%) with the ability to maintain sterility or restore male fertility of M and C CMS types, as well as with the combining ability from ultrahigh to good (32.6%) fell into the group with the flowering period duration of 51-55 days. According to the results of the harvested grain moisture assessment, the hybrids ♀(РГС246с × OL213) × ♂92с5986·2·3, ♀714М  ×  ♂1/67-1 and ♀714М  ×  ♂92н136-4, with the values of 13, 6%, 13.9%, 14.0%, respectively, were identified. The hybrids ♀714М × ♂1/67- 1 and ♀(OL563С × KL1392) × ♂92с0653 2 1 2 were characterized by the maximum value of the selection index, i.e. 5.03 and 5.13, respectively.Conclusions. The results of the studies showed the breeding value of rediploid lines as an initial material for hybrid maize breeding. 

scholarly journals Genetic diversity among tropical maize inbred lines as revealed by SSR markers

2020 ◽  
pp. 2010-2019
Author(s):  
Maizura Abu Sin ◽  
Ghizan Saleh ◽  
Nur Ashikin Psyquay Abdullah ◽  
Pedram Kashiani
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Inbred Lines ◽  
Hybrid Breeding ◽  
Heterotic Groups ◽  
Breeding Programs ◽  
Maize Inbred Lines

Genetic diversity and phenotypic superiority are important attributes of parental inbred lines for use in hybrid breeding programs. In this study, genetic diversity among 30 maize (Zea mays L.) inbred lines comprising of 28 introductions from the International Maize and Wheat Improvement Center (CIMMYT), one from Indonesia and a locally developed, were evaluated using 100 simple sequence repeat (SSR) markers, as early screening for potential parents of hybrid varieties. All markers were polymorphic, with a total of 550 unique alleles detected on the 100 loci from the 30 inbred lines. Allelic richness ranged from 2 to 13 per locus, with an average of 5.50 alleles (na). Number of effective alleles (ne) was 3.75 per locus, indicating their high effectiveness in revealing diversity among inbred lines. Average polymorphic information content (PIC) was 0.624, with values ranging from 0.178 to 0.874, indicating high informativeness of the markers. High gene diversity was observed on Chromosomes 8 and 4, with high number of effective alleles, indicating their potential usefulness for QTL analysis. The UPGMA dendrogram constructed identified four heterotic groups within a similarity index of 0.350, indicating that these markers were able to group the inbred lines. The three-dimensional PCoA plot also supports the dendrogram grouping, indicating that these two methods complement each other. Inbred lines in different heterotic groups have originated from different backgrounds and population sources. Information on genetic diversity among the maize inbred lines are useful in developing strategies exploiting heterosis in breeding programs

scholarly journals Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Dagne Wegary ◽  
Adefris Teklewold ◽  
Boddupalli M. Prasanna ◽  
Berhanu T. Ertiro ◽  
Nikolaos Alachiotis ◽  
...  
Keyword(s):  
Population Structure ◽  
Candidate Genes ◽  
Genetic Relatedness ◽  
Inbred Lines ◽  
Snp Markers ◽  
Pedigree Information ◽  
Selective Sweeps ◽  
Genetic Purity ◽  
Heterotic Groups ◽  
Maize Inbred Lines

Abstract Little is known on maize germplasm adapted to the African highland agro-ecologies. In this study, we analyzed high-density genotyping by sequencing (GBS) data of 298 African highland adapted maize inbred lines to (i) assess the extent of genetic purity, genetic relatedness, and population structure, and (ii) identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to highland environments. Nearly 91% of the pairs of inbred lines differed by 30–36% of the scored alleles, but only 32% of the pairs of the inbred lines had relative kinship coefficient <0.050, which suggests the presence of substantial redundancy in allelic composition that may be due to repeated use of fewer genetic backgrounds (source germplasm) during line development. Results from different genetic relatedness and population structure analyses revealed three different groups, which generally agrees with pedigree information and breeding history, but less so by heterotic groups and endosperm modification. We identified 944 single nucleotide polymorphic (SNP) markers that fell within 22 selective sweeps that harbored 265 protein-coding candidate genes of which some of the candidate genes had known functions. Details of the candidate genes with known functions and differences in nucleotide diversity among groups predicted based on multivariate methods have been discussed.

Microsatellite marker-based genetic diversity of tropical-adapted shrunken-2 maize inbred lines and its relationship with normal endosperm inbred lines of known heterotic classification

2021 ◽  
pp. 1-8
Author(s):  
J. E. Iboyi ◽  
A. Abe ◽  
V. O. Adetimirin
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Inbred Lines ◽  
Heterotic Group ◽  
Germplasm Management ◽  
Maize Breeding ◽  
Heterotic Groups ◽  
Maize Population ◽  
Maize Inbred Lines

Abstract Knowledge of the genetic diversity and relationships among maize inbred lines can facilitate germplasm management and plant breeding programmes. The study investigated the level of genetic diversity among S6 lines developed from a tropical-adapted shrunken-2 (sh-2) maize population and their relationship with normal endosperm tropical inbred lines of known heterotic groups. Ninety-one sh-2 maize inbred lines (UI1-UI91) developed in the University of Ibadan super-sweet Maize Breeding Programme were genotyped at 30 simple sequence repeat (SSR) loci, alongside five normal endosperm maize inbred lines viz. TZi3, TZi4, TZi10, TZi12 and TZi15, four of which belong to two heterotic groups. Twenty-three SSR markers were polymorphic and detected a total of 61 alleles, with a range of 2–7 and an average of 2.65 alleles per locus. The polymorphic information content ranged from 0.12 in bnlg1937 to 0.77 in phi126, with an average of 0.36. The gene diversity (He) averaged 0.43. Cluster analysis resulted in five groups consisting of 16, 36, 17, 23 and 3 inbred lines, with one sh-2 line ungrouped. TZi 12 and TZi 15, both of which are of the same heterotic group, clustered with TZi 3 of another heterotic group. Considerable genetic diversity exists among the 96 inbred lines. Only two of the five normal endosperm lines shared clusters with the sh-2 lines. The clustering of the normal endosperm inbred lines is not related to their established heterotic patterns. Inbred lines in two clusters offer the possibility of guiding the exploitation of heterosis among the sh-2 lines.

scholarly journals Changes of genetic diversity of maize inbred lines over four decades of hybrid breeding in the Bc institute revealed by SSR markers

Genetika ◽  
2015 ◽  
Vol 47 (1) ◽  
pp. 233-243
Author(s):  
Ivica Buhinicek ◽  
Mirko Jukic ◽  
Hrvoje Sarcevic ◽  
Jerko Gunjaca ◽  
Zdravko Kozic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Inbred Lines ◽  
Hybrid Breeding ◽  
Maize Breeding ◽  
Hybrid Production ◽  
The Past ◽  
Maize Inbred Lines ◽  
Heterotic Pattern ◽  
Private Alleles

In this paper, changes of genetic diversity of the most important maize inbred lines used for hybrid production within the Bc Institute in the 1970s, 1980s, 1990s and 2000s were examined using the SSR markers. The average number of alleles per SSR locus was 3.14, 3.43, 3.07 and 3.25 for lines from 1970s, 1980s, 1990s and 2000s, whereas the number of private alleles for the same four decades was 8, 4, 0 and 6, respectively. Mean genetic distance among inbreds within decades steadily decreased over time from 0.64 in 1970s to 0.57 in 2000s, but the observed differences were not statistically significant. The clustering of the studied inbred lines indicates the exploitation of a known BSSS x LSC heterotic pattern within the Bc Institute maize breeding program. The overall results show that recycled inbred lines within these pools do not decline in genetic variation over the past 40 years.

Retrotransposon-related genetic distance among inbred lines of sweet corn (Zea mays var. saccharata) and hybrid performance

2016 ◽  
Vol 16 (1) ◽  
pp. 50-58
Author(s):  
Georgi Bonchev ◽  
Lydia Shtereva ◽  
Rumiana Vassilevska-Ivanova
Keyword(s):  
Genetic Diversity ◽  
Sweet Corn ◽  
Correlation Study ◽  
Inbred Lines ◽  
Genetic Distances ◽  
Hybrid Performance ◽  
Maize Breeding ◽  
Relative Contribution ◽  
Maize Inbred Lines ◽  
Heterosis Effect

AbstractHeterosis is a main force underlying the hybrid seed industry in maize. Our experimental approach consists of a correlation study between retrotransposon-related genetic distances between parental inbred lines and hybrid performance. The assumption is that, at least for certain traits, heterosis results from genome rearrangements, largely related to retrotransposon insertions and/or removals. Fifteen maize inbred lines and one F1 hybrid, representative of the genetic diversity among sweet corn and field corn lines were screened for polymorphism by retrotransposon microsatellite amplified polymorphism markers. DNA fingerprints served as row data for estimating genetic diversity of maize inbred lines and its correlation with the heterotic effect in their hybrids. A correlation between phenotypic and molecular distances was evident only at the level of individual inbred lines. Weak correlation between genetic distances and heterosis effect was observed for the average of all inbred lines. Phenotypic distances negatively correlated with heterosis for insertion height, diameter of the ear and number of kernel rows per ear. The relative contribution of each inbred line to heterosis in its derived hybrids was also estimated. Accordingly, we identified inbred lines with increased genetic distances that mostly add to the heterosis effect in their hybrids and that we recommend as prospective to be used in maize breeding programmes.

Assessment of genetic diversity in Narbon vetch (Vicia narbonensis L.) germplasm using morphological and molecular markers

2018 ◽  
Vol 69 (9) ◽  
pp. 904 ◽  
Author(s):  
Siwar Bouabid ◽  
H. Chennaoui Kourda ◽  
A. Boussaha ◽  
M. Ben Naceur ◽  
A. Zoghlami Khélil
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Germplasm Management ◽  
Vicia Narbonensis ◽  
High Level ◽  
Differentiation Index ◽  
Simple Sequence

Narbon vetch (Vicia narbonensis L.) is a promising forage legume with good resistance to cold and drought. The assessment of genetic diversity of Narbon vetch is an essential component in germplasm management. In this study, we analysed the genetic diversity of 13 local and introduced Narbon vetch accessions from three continents using 27 morphological traits and 13 simple sequence repeat (SSR) markers. Significant differences among accessions for morphological and phenological traits were observed. The SSR markers showed a total of 126 alleles with a mean number of two alleles per locus. Polymorphic information content values were in the range of 0.772–0.915 with an average of 0.858. A high level of diversity (Nei’s genetic differentiation index of 59) was observed among accessions. Analysis of genetic distances separated the studied accessions into three groups based on both morphological and SSR markers. Cluster analysis of the SSR markers separated the accessions into three groups according to geographical origin. The Tunisian populations shared the same morphological traits but differed genetically from each other and were similar to those from Lebanon. A significant correlation was detected between morphological traits and SSR markers. The results suggested that SSR markers can be used to efficiently distinguish Narbon vetch accessions and estimate their genetic diversity.

scholarly journals The Usefulness of Molecular Markers Approach for Developing Heterotic Groups in Maize

2014 ◽  
Vol 1 (2) ◽  
pp. 4-10
Author(s):  
Willy B Suwarno
Keyword(s):  
Molecular Markers ◽  
Genetic Distance ◽  
Genetic Background ◽  
Inbred Lines ◽  
Genetic Distances ◽  
Heterotic Group ◽  
Maize Breeding ◽  
Heterotic Groups ◽  
Good Opportunity

The phenomenon of heterosis provides a greatopportunity for plant breeders to gain greaterperformance and yield in the hybrids compared to theirinbred line parents. In most cross-pollinated crops likemaize, heterosis plays an important role as theperformance of the hybrids is of a great value. Heterosisgain much interest until recently and current studies stillattempt to elucidateone of these is utilizing molecularmarkers to estimate genetic distances among inbredlines followed by developing putative groups. In a welldened heterotic group, between-groups mating areexpected to produce better hybrids than within-groupsmating. Some studies of marker-aided heterotic groupdevelopment resulted in functional heterotic groups;while some other reported that the groups failed toprovide evidence of heterosis in the hybrids.Considering the prediction of hybrids' performance willdepend on genetic background of inbred lines, andmarkers technology are continuously improved, there isstill a good opportunity to obtain useful heterotic groupsfor a particular breeding population.Keywords: maize breeding, genetic distance, heterosis,molecular markers.

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