Leaf transcriptome analysis of Lancaster versus other heterotic groups’ maize inbred lines revealed different regulation of cold‐responsive genes

2021 ◽  
Author(s):  
Bojana Banović Đeri ◽  
Manja Božić ◽  
Dragana Dudić ◽  
Ivan Vićić ◽  
Marija Milivojević ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Inbred Lines ◽  
Heterotic Groups ◽  
Maize Inbred Lines ◽  
Leaf Transcriptome

scholarly journals Evaluation of Yield-Based Low Nitrogen Tolerance Indices for Screening Maize (Zea mays L.) Inbred Lines

Agronomy ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 240 ◽  
Author(s):  
Zhixin Zhao ◽  
Kunhui He ◽  
Zhiqian Feng ◽  
Yanan Li ◽  
Liguo Chang ◽  
...  
Keyword(s):  
Grain Yield ◽  
Geometric Mean ◽  
Inbred Lines ◽  
Shaanxi Province ◽  
High Yield ◽  
Tolerance Index ◽  
Heterotic Groups ◽  
Maize Inbred Lines ◽  
Low Nitrogen Tolerance ◽  
Low Nitrogen

To screen the desired criterion to identify desirable genotypes and select genotypes best suited to limited nitrogen availability in order to facilitate the practice of low-nitrogen-tolerant breeding in maize, the response of 31 maize inbred lines, containing four control inbred lines (PH6WC, PH4CV, Zheng58, and Chang7-2) and others selected from the Shaan A and Shaan B heterotic groups cultivated at Northwest A&F University (Yangling, Shaanxi, China), were evaluated. The experiment was conducted following a split plot design with two replications during three growing seasons (2015, 2016, and 2017) under both high nitrogen (HN) and low nitrogen (LN) conditions at the Yulin and Yangling in Shaanxi Province, China. Seven screening indices, based on grain yield under two contrasting nitrogen (N) conditions, the stress susceptibility index (SSI), yield stability index (YSI), mean productivity (MP), geometric mean productivity (GMP), stress tolerance index (STI), harmonic mean (HM), and low nitrogen tolerance index (LNTI), were computed to assess the overall index that accurately screened the desirable genotypes. The results of the correlation analyses and principal component analysis showed that MP, GMP, HM and STI were correlated with grain yield significantly and positively under contrasting N conditions, and were able to accurately discriminate the desirable genotypes. Compared with the control inbred lines, many inbred lines selected from the Shaan A and Shaan B groups showed a higher LN tolerance. This shows that we can effectively improve the LN tolerance of maize inbred lines through LN screening. Based on the screening indices, the three-dimensional diagram and genotype and genotype × environment (GGE) biplots are agreed with this results, and we identified KA105, KB081, KA225, 91227, and 2013KB-47 as the desired genotypes that have the potential to be used to breed a high yield and stable hybrid.

scholarly journals Agronomic and molecular evaluation of maize inbred lines for drought tolerance

2016 ◽  
Vol 14 (4) ◽  
pp. e0711 ◽  
Author(s):  
Sanja Mikić ◽  
Miroslav Zorić ◽  
Dušan Stanisavljević ◽  
Ankica Kondić-Špika ◽  
Ljiljana Brbaklić ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Grain Yield ◽  
Maize Yield ◽  
Field Trials ◽  
Inbred Lines ◽  
Partial Least Square ◽  
Least Square ◽  
Maize Breeding ◽  
Heterotic Groups ◽  
Maize Inbred Lines

Drought is a severe threat to maize yield stability in Serbia and other temperate Southeast European countries occurring occasionally but with significant yield losses. The development of resilient genotypes that perform well under drought is one of the main focuses of maize breeding programmes. To test the tolerance of newly developed elite maize inbred lines to drought stress, field trials for grain yield performance and anthesis silk interval (ASI) were set in drought stressed environments in 2011 and 2012. Inbred lines performing well under drought, clustered into a group with short ASI and a smaller group with long ASI, were considered as a potential source for tolerance. The former contained inbreds from different heterotic groups and with a proportion of local germplasm. The latter consisted of genotypes with mixed exotic and Lancaster germplasm, which performed better in more drought-affected environments. Three inbreds were selected for their potential drought tolerance, showing an above-average yield and small ASI in all environments. Association analysis indicated significant correlations between ASI and grain yield and three microsatellites (bnlg1525, bnlg238 and umc1025). Eight alleles were selected for their favourable concurrent effect on yield increase and ASI decrease. The proportion of phenotypic variation explained by the markers varied across environments from 5.7% to 22.4% and from 4.6% to 8.1% for ASI and yield, respectively. The alleles with strongest effect on performance of particular genotypes and their interactions in specific environments were identified by the mean of partial least square interactions analysis indicating potential suitability of the makers for tolerant genotype selection.

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.

Genome-wide transcriptome analysis of two maize inbred lines under drought stress

2009 ◽  
Vol 72 (4-5) ◽  
pp. 407-421 ◽  
Author(s):  
Jun Zheng ◽  
Junjie Fu ◽  
Mingyue Gou ◽  
Junling Huai ◽  
Yunjun Liu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Transcriptome Analysis ◽  
Inbred Lines ◽  
Maize Inbred Lines ◽  
Genome Wide

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 Association analysis of agronomic traits with microsatellites in maize inbred lines

Genetika ◽  
2018 ◽  
Vol 50 (2) ◽  
pp. 379-394
Author(s):  
Sanja Mikic ◽  
Ankica Kondic-Spika ◽  
Ljiljana Brbaklic ◽  
Dusan Stanisavljevic ◽  
Dragana Trkulja ◽  
...  
Keyword(s):  
Population Structure ◽  
Microsatellite Markers ◽  
Association Analysis ◽  
Agronomic Traits ◽  
Inbred Lines ◽  
Linkage Disequilibrium Mapping ◽  
Heterotic Groups ◽  
Local Conditions ◽  
Maize Inbred Lines ◽  
Trait Associations

Association analysis or linkage disequilibrium mapping is a method for identification of quantitative trait loci (QTLs) in a panel of divergent unrelated individuals based on historical recombinations during a crop?s domestication and selection. It should account for the population structure, which can be the result of adaptation to local conditions or selection, to reduce the possibility of declaring false-positive associations. The aim of this study was to determine potentially significant and consistent associations between markers and agronomic important maize (Zea mays L.) traits using association analysis in a diverse breeding material that can be ultimately implemented in maize selection. To this end, 96 maize inbred lines were evaluated in field trials at three locations in Serbia for eleven agronomic traits and analysed with microsatellite markers. Twenty five microsatellites were used to assess the population structure using Bayesian model-based clustering method and to test the significance of associations between the markers and the traits with general (GLM) and mixed linear (MLM) models. The cluster analysis divided maize inbred lines in four subpopulations, corresponding to the BSSS (Iowa Stiff Stalk Synthetic), LSC (Lancaster Sure Crop), Iodent heterotic groups and exotic and independent germplasm. The models identified associations between twenty five microsatellite markers and eleven agronomic traits, resulting in 133 and 71 associations across the environments for GLM and MLM, respectively. Some of the identified marker-trait associations were significant and consistent in several environments. The associations stable in several environments were identified between the markers bnlg1067 and two flowering traits; nc005 and bnlg434 and plant height, bnlg434 and ear height; bnlg1643 and umc1127 and leaf number, bnlg1360 and ear diameter; umc1019 and umc1506 and number of rows per ear; bnlg2305 and bnlg1451 and ear length, and between bnlg1175 and thousand-kernel weight. The results of this study indicate that these microsatellites could be used in marker-assisted selection of inbred lines, after validation of the marker-trait associations and testing combining abilities of the inbreds during hybrid development.

scholarly journals Genetic Diversity and Heterotic Orientation of South Africa Maize Inbred Lines Towards Tropical and Temperate Testers

2021 ◽  
Author(s):  
Siphiwokuhle Funani Shandu ◽  
John Derera ◽  
Kingston Mashingaidze ◽  
Edmore Gasura
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Grain Yield ◽  
Combining Ability ◽  
Molecular Genetic ◽  
Inbred Lines ◽  
Genetic Distances ◽  
Specific Combining Ability ◽  
Heterotic Groups ◽  
Maize Inbred Lines

Abstract An efficient hybrid breeding program defines and utilizes few heterotic groups. The objectives of this study were to determine genetic diversity and alignment of South Africa maize inbred lines collection towards tropical and temperate testers. Forty-two maize inbred lines were genotyped with 56110 single nucleotide polymorphism (SNP) DNA markers, using the Illumina MaizeSNP50 Bead chip. The 42 lines were crossed to two tropical and two temperate inbred line testers. The testcrosses were evaluated across seven environments, in South Africa, during 2014-2016. Genotypes and specific combining ability (SCA) effects of hybrids were significantly different (P<0.05) for grain yield. There was a weak correlation between molecular genetic distances and both grain yield mean and specific combining ability effects of hybrids, indicating that productivity of maize inbred lines could not be reliably determined based on molecular genetic distances. The SCA data was capable of classifying these maize inbred lines into three heterotic groups with respect to both tropical and temperate testers. Only a few lines could not be grouped on the basis of SCA data. The study also indicated high level of diversity among the maize inbred lines, which was shown by both the dendogram and molecular genetic distances. The SNP marker data classified the inbred lines into 11 clusters that could be simplified into three major groups of normal maize endosperm and two groups of quality protein maize (QPM) endosperm types. However, the SNP data indicated that maize lines were more aligned towards tropical than temperate inbred testers. This information would be useful for simplifying heterotic classification of the lines with profound implications for breeding progress.

Genetic diversity analysis of 119 Canadian maize inbred lines based on pedigree and simple sequence repeat markers

2011 ◽  
Vol 91 (4) ◽  
pp. 651-661 ◽  
Author(s):  
L. M. Reid ◽  
K. Xiang ◽  
X. Zhu ◽  
B. R. Baum ◽  
S. J. Molnar
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inbred Lines ◽  
Diversity Analysis ◽  
Sequence Repeat ◽  
Heterotic Groups ◽  
Simple Sequence Repeat Markers ◽  
Genetic Diversity Analysis ◽  
Maize Inbred Lines ◽  
Simple Sequence

Reid, L. M., Xiang, K., Zhu, X., Baum, B. R. and Molnar, S. J. 2011. Genetic diversity analysis of 119 Canadian maize inbred lines based on pedigree and simple sequence repeat markers. Can. J. Plant Sci. 91: 651–661. Since the early 1920s Agriculture and Agri-Food Canada (AAFC) has been developing maize varieties and inbred lines adapted to the early maize growing regions. These inbreds represent a large group of genetically diverse genotypes; however, many of the inbreds are of unknown heterotic backgrounds. The purpose of this study was to classify 119 elite maize inbred lines released from AAFC into heterotic groups using both pedigree data and simple sequence repeat (SSR) markers and also to explore the consistency among different classification analyses. Pedigree analysis placed the inbred lines into eight groups, six of which corresponded to known major heterotic groups representing Iowa Stiff Stalk Synthetic (BSSS), European flint, Lancaster, Minnesota 13, Early Butler, and Iodent; the two remaining groups consisted of germplasm derived mostly from Pioneer 3990 or Pioneer 3994 sources. Simple sequence repeat analysis of 105 loci resulted in a clustering of the inbreds into 10 groups. In comparison with the grouping based on pedigree, the SSR clustering groups had some discrepancies and groups of genetically similar germplasm, based on pedigree, could not always be confirmed with molecular markers. The results of this study will allow researchers and maize breeders to make more informed decisions on the use of these inbreds in breeding programs.

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