scholarly journals Marker-Assisted Introgression in Backcross Breeding Programs

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1923-1932 ◽  
Author(s):  
Peter M Visscher ◽  
Chris S Haley ◽  
Robin Thompson
Keyword(s):  
Quantitative Trait ◽  
Genetic Model ◽  
Phenotypic Selection ◽  
Inbred Lines ◽  
Breeding Programs ◽  
Coupling Phase ◽  
Breed Difference ◽  
Backcross Populations ◽  
Backcross Breeding ◽  
Marker Spacing

The efficiency of marker-assisted introgression in backcross populations derived from inbred lines was investigated by simulation. Background genotypes were simulated assuming that a genetic model of many genes of small effects in coupling phase explains the observed breed difference and variance in backcross populations. Markers were efficient in introgression backcross programs for simultaneously introgressing an allele and selecting for the desired genomic background. Using a marker spacing of 10–20 cM gave an advantage of one to two backcross generations selection relative to random or phenotypic selection. When the position of the gene to be introgressed is uncertain, for example because its position was estimated from a trait gene mapping experiment, a chromosome segment should be introgressed that is likely to include the allele of interest. Even for relatively precisely mapped quantitative trait loci, flanking markers or marker haplotypes should cover ∼10–20 cM around the estimated position of the gene, to ensure that the allele frequency does not decline in later backcross generations.

scholarly journals A general mixture model approach for mapping quantitative trait loci from diverse cross designs involving multiple inbred lines

2000 ◽  
Vol 75 (3) ◽  
pp. 345-355 ◽  
Author(s):  
YUEFU LIU ◽  
ZHAO-BANG ZENG
Keyword(s):  
Quantitative Trait Loci ◽  
Statistical Method ◽  
Mixture Model ◽  
Quantitative Trait ◽  
Genetic Model ◽  
General Procedure ◽  
Inbred Lines ◽  
Design Matrix ◽  
Trait Loci ◽  
Parental Lines

Most current statistical methods developed for mapping quantitative trait loci (QTL) based on inbred line designs apply to crosses from two inbred lines. Analysis of QTL in these crosses is restricted by the parental genetic differences between lines. Crosses from multiple inbred lines or multiple families are common in plant and animal breeding programmes, and can be used to increase the efficiency of a QTL mapping study. A general statistical method using mixture model procedures and the EM algorithm is developed for mapping QTL from various cross designs of multiple inbred lines. The general procedure features three cross design matrices, W, that define the contribution of parental lines to a particular cross and a genetic design matrix, D, that specifies the genetic model used in multiple line crosses. By appropriately specifying W matrices, the statistical method can be applied to various cross designs, such as diallel, factorial, cyclic, parallel or arbitrary-pattern cross designs with two or multiple parental lines. Also, with appropriate specification for the D matrix, the method can be used to analyse different kinds of cross populations, such as F2 backcross, four-way cross and mixed crosses (e.g. combining backcross and F2). Simulation studies were conducted to explore the properties of the method, and confirmed its applicability to diverse experimental designs.

Empirical Nonparametric Bootstrap Strategies in Quantitative Trait Loci Mapping: Conditioning on the Genetic Model

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 525-535
Author(s):  
Claude M Lebreton ◽  
Peter M Visscher
Keyword(s):  
Quantitative Trait Loci ◽  
Confidence Interval ◽  
Confidence Intervals ◽  
Quantitative Trait ◽  
Genetic Factors ◽  
Genetic Model ◽  
Original Data ◽  
Nonparametric Bootstrap ◽  
Test Protocol ◽  
Trait Loci

AbstractSeveral nonparametric bootstrap methods are tested to obtain better confidence intervals for the quantitative trait loci (QTL) positions, i.e., with minimal width and unbiased coverage probability. Two selective resampling schemes are proposed as a means of conditioning the bootstrap on the number of genetic factors in our model inferred from the original data. The selection is based on criteria related to the estimated number of genetic factors, and only the retained bootstrapped samples will contribute a value to the empirically estimated distribution of the QTL position estimate. These schemes are compared with a nonselective scheme across a range of simple configurations of one QTL on a one-chromosome genome. In particular, the effect of the chromosome length and the relative position of the QTL are examined for a given experimental power, which determines the confidence interval size. With the test protocol used, it appears that the selective resampling schemes are either unbiased or least biased when the QTL is situated near the middle of the chromosome. When the QTL is closer to one end, the likelihood curve of its position along the chromosome becomes truncated, and the nonselective scheme then performs better inasmuch as the percentage of estimated confidence intervals that actually contain the real QTL's position is closer to expectation. The nonselective method, however, produces larger confidence intervals. Hence, we advocate use of the selective methods, regardless of the QTL position along the chromosome (to reduce confidence interval sizes), but we leave the problem open as to how the method should be altered to take into account the bias of the original estimate of the QTL's position.

scholarly journals A New Breeding Strategy towards Introgression and Characterization of Stay-Green QTL for Drought Tolerance in Sorghum

Agriculture ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 598
Author(s):  
Nasrein Mohamed Kamal ◽  
Yasir Serag Alnor Gorafi ◽  
Hanan Abdeltwab ◽  
Ishtiag Abdalla ◽  
Hisashi Tsujimoto ◽  
...  
Keyword(s):  
Phenotypic Expression ◽  
Phenotypic Selection ◽  
Breeding Strategy ◽  
Stay Green ◽  
Breeding Programs ◽  
The Public ◽  
Drought Tolerant ◽  
Selection Step ◽  
The Cost

Several marker-assisted selection (MAS) or backcrossing (MAB) approaches exist for polygenic trait improvement. However, the implementation of MAB remains a challenge in many breeding programs, especially in the public sector. In MAB introgression programs, which usually do not include phenotypic selection, undesired donor traits may unexpectedly turn up regardless of how expensive and theoretically powerful a backcross scheme may be. Therefore, combining genotyping and phenotyping during selection will improve understanding of QTL interactions with the environment, especially for minor alleles that maximize the phenotypic expression of the traits. Here, we describe the introgression of stay-green QTL (Stg1–Stg4) from B35 into two sorghum backgrounds through an MAB that combines genotypic and phenotypic (C-MAB) selection during early backcross cycles. The background selection step is excluded. Since it is necessary to decrease further the cost associated with molecular marker assays, the costs of C-MAB were estimated. Lines with stay-green trait and good performance were identified at an early backcross generation, backcross two (BC2). Developed BC2F4 lines were evaluated under irrigated and drought as well as three rainfed environments varied in drought timing and severity. Under drought conditions, the mean grain yield of the most C-MAB-introgression lines was consistently higher than that of the recurrent parents. This study is one of the real applications of the successful use of C-MAB for the development of drought-tolerant sorghum lines for drought-prone areas.

Genetic and Nongenetic Bases for the L-Shaped Distribution of Quantitative Trait Loci Effects

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1773-1787 ◽  
Author(s):  
Bruno Bost ◽  
Dominique de Vienne ◽  
Frédéric Hospital ◽  
Laurence Moreau ◽  
Christine Dillmann
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Population Size ◽  
Quantitative Trait ◽  
Metabolic Flux ◽  
Genetic Model ◽  
Small Population ◽  
Additive Genetic Model ◽  
Metabolic Mechanism ◽  
Qtl Effects

Abstract The L-Shaped distribution of estimated QTL effects (R2) has long been reported. We recently showed that a metabolic mechanism could account for this phenomenon. But other nonexclusive genetic or nongenetic causes may contribute to generate such a distribution. Using analysis and simulations of an additive genetic model, we show that linkage disequilibrium between QTL, low heritability, and small population size may also be involved, regardless of the gene effect distribution. In addition, a comparison of the additive and metabolic genetic models revealed that estimates of the QTL effects for traits proportional to metabolic flux are far less robust than for additive traits. However, in both models the highest R2's repeatedly correspond to the same set of QTL.

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

BMC Genomics ◽  
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.

scholarly journals Metabolome-scale genome-wide association studies reveal chemical diversity and genetic control of maize specialized metabolites

2018 ◽  
Author(s):  
Zhou Shaoqun ◽  
Karl A. Kremling ◽  
Bandillo Nonoy ◽  
Richter Annett ◽  
Ying K. Zhang ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Citrate Synthase ◽  
Association Studies ◽  
Inbred Lines ◽  
Chemical Diversity ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Single Linkage ◽  
Genome Wide ◽  
Maize Varieties

One Sentence SummaryHPLC-MS metabolite profiling of maize seedlings, in combination with genome-wide association studies, identifies numerous quantitative trait loci that influence the accumulation of foliar metabolites.AbstractCultivated maize (Zea mays) retains much of the genetic and metabolic diversity of its wild ancestors. Non-targeted HPLC-MS metabolomics using a diverse panel of 264 maize inbred lines identified a bimodal distribution in the prevalence of foliar metabolites. Although 15% of the detected mass features were present in >90% of the inbred lines, the majority were found in <50% of the samples. Whereas leaf bases and tips were differentiated primarily by flavonoid abundance, maize varieties (stiff-stalk, non-stiff-stalk, tropical, sweet corn, and popcorn) were differentiated predominantly by benzoxazinoid metabolites. Genome-wide association studies (GWAS), performed for 3,991 mass features from the leaf tips and leaf bases, showed that 90% have multiple significantly associated loci scattered across the genome. Several quantitative trait locus hotspots in the maize genome regulate the abundance of multiple, often metabolically related mass features. The utility of maize metabolite GWAS was demonstrated by confirming known benzoxazinoid biosynthesis genes, as well as by mapping isomeric variation in the accumulation of phenylpropanoid hydroxycitric acid esters to a single linkage block in a citrate synthase-like gene. Similar to gene expression databases, this metabolomic GWAS dataset constitutes an important public resource for linking maize metabolites with biosynthetic and regulatory genes.

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

2019 ◽  
Vol 30 (1) ◽  
pp. 25-33
Author(s):  
E.A. Rossi ◽  
M. Ruiz ◽  
M. Di Renzo ◽  
N.C. Bonamico
Keyword(s):  
Population Structure ◽  
Morphological Traits ◽  
Phenotypic Diversity ◽  
Genotypic Diversity ◽  
Inbred Lines ◽  
Environmental Adaptation ◽  
Procrustes Analysis ◽  
Phenotypic Characterization ◽  
Breeding Programs ◽  
Maize Inbred Lines

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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