GENOTYPIC DIVERSITY IN 291 MAIZE LINES FROM CIMMYT AND PHENOTYPIC CHARACTERIZATION IN SOUTHERN CORDOBA, ARGENTINA

CIMMYT maize inbred lines (CMLs) are freely distributed to breeding programs around the world. Better information on phenotypic and genotypic diversity may provide guidance to breeders on how to use more efficiently the CMLs in their breeding programs. In this study a group of 291 CIMMYT maize inbred lines, was phenotyped by nine agro-morphological traits in south Córdoba, Argentina and genotyped using 18,082 SNPs. Based on the geographic information and the environmental adaptation, 291 CMLs were classified into eight subgroups. Anthesis-silking interval (IAE) was the trait with higher phenotypic diversity. A 40% of maize inbred lines, with IAE less than five days, show a good adaptation to growing conditions in south Córdoba, Argentina. The low phenotypic variation explained by environmental adaptation subgroups indicates that population structure is only a minor factor contributing to phenotypic diversity in this panel. Principal component analysis (ACP) allowed us to obtain phenotypic and genotypic orderings. Generalized procrustes analysis (APG) indicated a 60% consensus between both data type from the total panel of maize lines. In each environmental adaptation subgroup, the APG consensus was higher. This result, which might indicate linkage disequilibrium between SNPs markers and the genes controlling these agro-morphological traits, is promising and could be used as an initial tool in the identification of Quantitative Trait Loci (QTL). Information on genetic diversity, population structure and phenotypic diversity in local environments will help maize breeders to better understand how to use the current CIMMYT maize inbred lines group. Key words: broad-sense heritability, multivariate analysis, SNPs, agro-morphological traits.

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Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil

BMC Genomics ◽

10.1186/s12864-021-08127-7 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Sirlene Viana de Faria ◽

Leandro Tonello Zuffo ◽

Wemerson Mendonça Rezende ◽

Diego Gonçalves Caixeta ◽

Hélcio Duarte Pereira ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Inbred Lines ◽

Breeding Program ◽

Tropical Maize ◽

Maize Breeding ◽

Breeding Programs ◽

The Public ◽

Maize Inbred Lines

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

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Phenotypic diversity and carcass quality of creole goats with genetic potential for resistance to infection caused by worm

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2018000700009 ◽

2018 ◽

Vol 53 (7) ◽

pp. 849-857

Author(s):

Vanessa dos Santos Neri ◽

José Lindenberg Rocha Sarmento ◽

Laylson da Silva Borges ◽

Tatiana Saraiva Torres ◽

Luciano Silva Sena ◽

...

Keyword(s):

Body Weight ◽

Phenotypic Diversity ◽

Phenotypic Characterization ◽

Carcass Quality ◽

Breeding Programs ◽

Genetic Groups ◽

Genetic Potential ◽

Resistance To Infection

Abstract: The objective of this work was to phenotypically characterize creole goats of the Moxotó, Azul, Canindé, Repartida, Marota, and Graúna breeds, comparing them with the Boer, Anglo Nubian, and Alpine exotic breeds, to identify the genetic groups of greater potential for carcass quality and resistance to infection caused by worm. Data on morphometric measurements were obtained for the count of worm eggs in grams of feces (WEGF), Famacha score, carcass measurements, and body weight from 308 animals, in a farm in the state of Piauí, Brazil. Repartida goats showed the highest average for wither height (61.55 cm) and rump height (62.16 cm), and Moxotó goats had the greatest ear length (13.45 cm). The Moxotó breed showed the highest means for carcass and body weight. The lowest average for body weight was observed in Azul goats (24.35 kg), and the lowest WEGF was detected in Repartida goats (200 eggs per gram of feces). The average Famacha score was 2.77. Average linkage was the method that best summarized the information on the morphometric and carcass data. The use of morphometric and carcass measurements provides satisfactory results in the phenotypic characterization of the animals. The Brazilian creole goats, which are considered resistant to worm infection and show high-quality carcass traits, may be indicated for conservation and genetic breeding programs.

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Microsatellite analysis of the correlation between molecular and morphological traits in assorted maize inbred lines

African Crop Science Journal ◽

10.4314/acsj.v17i3.54213 ◽

2010 ◽

Vol 17 (3) ◽

Author(s):

J Karanja ◽

NO Amugune ◽

J Ininda ◽

JN Kimatu ◽

JW Danson

Keyword(s):

Morphological Traits ◽

Inbred Lines ◽

Microsatellite Analysis ◽

Maize Inbred Lines

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Relationship between genetic markers and morphological traits in a maize inbred lines collection

Euphytica ◽

10.1007/bf01677953 ◽

1995 ◽

Vol 84 (2) ◽

pp. 145-154 ◽

Cited By ~ 22

Author(s):

A. Bar-Hen ◽

A. Charcosset ◽

M. Bourgoin ◽

J. Guiard

Keyword(s):

Genetic Markers ◽

Morphological Traits ◽

Inbred Lines ◽

Maize Inbred Lines

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Retraction Note to: An analysis of population structure and linkage disequilibrium using multilocus data in 187 maize inbred lines

Molecular Breeding ◽

10.1007/s11032-011-9556-z ◽

2011 ◽

Vol 28 (1) ◽

pp. 135-135

Author(s):

Chuanxiao Xie ◽

Marilyn Warburton ◽

Mingshun Li ◽

Xinhai Li ◽

Muji Xiao ◽

...

Keyword(s):

Population Structure ◽

Linkage Disequilibrium ◽

Inbred Lines ◽

Maize Inbred Lines

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

Australian Journal of Crop Science ◽

10.21475/ajcs.20.14.12.1589.pdf ◽

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

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Analysis of Population Structure and Genetic Diversity among Canadian Maize Inbred Lines using SSR Markers

Korean Journal of Breeding Science ◽

10.9787/kjbs.2017.49.2.72 ◽

2017 ◽

Vol 49 (2) ◽

pp. 072-79

Author(s):

Tak Ki Hong ◽

Kyu Jin Sa ◽

Ju Kyong Lee

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Inbred Lines ◽

Maize Inbred Lines

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Karakterisasi Kemiripan Genetik Koleksi Inbrida Jagung Berdasarkan Marka Mikrosatelit

Jurnal AgroBiogen ◽

10.21082/jbio.v2n2.2006.p45-51 ◽

2016 ◽

Vol 2 (2) ◽

pp. 45 ◽

Cited By ~ 1

Author(s):

Marcia Bunga Pabendon ◽

M. Dahlan ◽

Sutrisno Sutrisno ◽

M. L.C. George

Keyword(s):

Ssr Markers ◽

Genetic Relationships ◽

Morphological Characters ◽

Inbred Lines ◽

Genetic Distances ◽

Breeding Programs ◽

Maize Inbred Lines ◽

Clear Differentiation ◽

Source Populations ◽

Crop Germplasm

<p class="p1">Information on genetic relationships among available crop germplasm such as maize inbred lines, has important implications to breeding programs. A set of 26 maize inbreds togeher with six standard lines from CIMMYT (CML51, CML292, CML202, CML206, CML236, dan CML396), was characterized using 26 SSR markers, which were coverage of the maize genomes. The objective of this study was to analyze genetic diversities among the Indonesian maize inbred collections. Polymorphism Information Content (PIC) value and the observed genetic distance indicated the existence of large variabilities among the inbreds. Cluster analysis based on 27% of the Jaccard’s similarity coefficient placed the inbreds into three groups. Genetic distances among all the possible pairs without the standard maize lines varied from 0.32 (KSX360F2-5-1-3-1v vs KSX2601F2-5-1-1-v) to 0.88 (PT963298-1-B-B-Bv vs Mr13). Cluster and Principal Coordinate Analysis of the genetic distances, revealed a clear differentiation of the inbred lines into groups according to their source populations. This clustering were consistent with those of the known pedigree records of the inbreds based on their morphological characters. These results support the use of morphological traits in the production of maize hybrids. The SSR markers proved to be effective to characterize, identify, and demonstrate genetic similarities among the maize inbred lines.</p>

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

Scientific Reports ◽

10.1038/s41598-019-49861-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

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.

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