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1.
Stich B Piepho HP Schulz B Melchinger AE 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,117(6):947-954
Association mapping promises to overcome the limitations of linkage mapping methods. The main objective of this study was to examine the applicability of multivariate association mapping with an empirical data set of sugar beet. A total of 111 diploid sugar beet inbreds was selected from the seed parent heterotic pool to represent a broad diversity with respect to sugar content (SC). The inbreds were genotyped with 26 simple sequence repeat markers chosen according to their map positions in proximity to previously identified quantitative trait loci for SC. For SC and beet yield (BY), the genotypic variances were highly significant (P < 0.01). Based on the global test of the bivariate mixed-model approach, four markers were significantly associated with SC, BY, or both at a false discovery rate of 0.025. All four markers were significantly (P < 0.05) associated with BY but only two with SC. The identification of markers associated with SC, BY, or both indicated that association mapping can be successfully applied in a sugar beet breeding context for detection of marker-phenotype associations. Furthermore, based on our results multivariate association mapping can be recommended as a promising tool to discriminate with a high mapping resolution between pleiotropy and linkage as reasons for co-localization of marker-phenotype associations for different traits. 相似文献
2.
Mapping QTL for production traits in segregating Piétrain pig populations using genome‐wide association study results of F2 crosses 下载免费PDF全文
In this study, genome‐wide association study (GWAS) results of porcine F2 crosses were used to map QTL in outcross Piétrain populations. For this purpose, two F2 crosses (Piétrain × Meishan, n = 304; Piétrain × Wild Boar, n = 291) were genotyped with the PorcineSNP60v2 BeadChip and phenotyped for the dressing yield, carcass length, daily gain and drip loss traits. GWASs were conducted in the pooled F2 cross applying single marker mixed linear models. For the investigated traits, between two and five (in total 15) QTL core regions, spanning 250 segregating SNPs around a significant trait‐associated peak SNP, were identified. The SNPs within the QTL core regions were subsequently tested for trait association in two outcross Piétrain populations consisting of 771 progeny‐tested boars and 210 sows with their own performance records. In the sow (boar) dataset, five (eight) of the 15 mapped QTL were validated. Hence, many QTL mapped in the F2 crosses (with Piétrain as a common founder breed) are still segregating in the current Piétrain breed. This confirms the usefulness of existing F2 crosses for mapping QTL that are still segregating in the recent founder breed generation. The approach utilizes the high power of an F2 cross to map QTL in a breeding population for which it is not guaranteed that they would be found using a GWAS in this population. 相似文献
3.
Diana D. Schwegler Wenxin Liu Manje Gowda Tobias Würschum Britta Schulz Jochen C. Reif 《Molecular breeding : new strategies in plant improvement》2013,31(2):279-287
Linkage mapping based on multiple-line crosses is a promising strategy for mapping quantitative trait loci (QTL) underlying important agronomic traits. The main goal of this survey was to study the advantages of QTL mapping across versus within biparental populations using experimental data from three connected sugar beet (Beta vulgaris L.) populations evaluated for beet yield and potassium and sodium content. For the combined analysis across populations, we used two approaches for cofactor selection. In Model A, we assumed identical cofactors for every segregating population. In contrast, in Model B we selected cofactors specific for every segregating population. Model A performed better than Model B with respect to the number of QTL detected and the total proportion of phenotypic variance explained. The QTL analyses across populations revealed a substantially higher number of QTL compared to the analyses of single biparental populations. This clearly emphasizes the potential to increase QTL detection power with a joint analysis across biparental populations. 相似文献
4.
E. Barzen W. Mechelke E. Ritter J. F. Seitzer F. Salamini 《The Plant journal : for cell and molecular biology》1992,2(4):601-611
An RFLP linkage map for the nine chromosomes of sugar beet (Beta vulgaris L. ssp. vulgaris var. altissima Doell) was constructed by using a segregating population from a cross between two plants which were heterozygous for several agronomically interesting characters. One hundred and eleven RFLP loci have been mapped to nine linkage groups using 92 genomic markers. The current RFLP map covers a total length of 540 cM. Evidence for the existence of a major gene for rhizomania resistance (Rr1) is given, together with its map position on linkage group IV in the interval between loci GS44 and GS28a. The presence of an RFLP fragment at the GS3d locus is, until now, the best molecular marker for rhizomania-resistant genotypes in segregating populations of sugar beet; GS3d is linked to Rr1 with 6.7 cM. The gene MM, controlling the polygerm/monogerm seed type, has been mapped on linkage group IX in a distal position at 4.2 cM from the locus GS7. The gene R controlling the hypocotyl colour maps to linkage group VII and does not recombine with the RFLP locus GS42. The inheritance of a group of RFLP loci revealed the possible presence of a translocation in the population used to establish the map. The data presented are discussed in relation to the possibility of using RFLP markers in sugar beet breeding. 相似文献
5.
B. E. Zehr J. W. Dudley J. Chojecki 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1992,84(5-6):704-708
Summary If molecular markers are to be routinely used in maize (Zea mays L.) breeding for selection of quantitative trait loci (QTL), then consistent marker-trait associations across breeding populations are needed, as are efficient methods for weighting information from different markers. Given 15 restriction fragment length polymorphism (RFLP) markers associated with grain yield in testcrosses of 220 [BS11(FR)C7 x FRMol7] F2 individuals to FRB73, separate weighting schemes were attempted in order to maximize the frequency of favorable marker genotypes associated with increased grain yield in selected F2 individuals and F2:S4 Unes. The following principles were apparent: (1) Differential weighting among markers, in addition to weighting individual marker genotypes on the basis of associated mean effects, should be emphasized when using markers to select in breeding populations. This is due to limited population sizes that can readily be handled. (2) Relatively few markers may need to be used to screen segregating populations (e.g., F2) of limited size for loci affecting complex traits, such as combining ability for grain yield, assuming prior knowledge of marker-QTL associations. Markers given greatest weight (largest estimates of associated effects) will determine most selections. (3) When marker-based selection is among individuals at higher levels of inbreeding (e.g., S4) within selected families, more markers need to be used in screening because those associated with relatively small effects have an increased chance of affecting selection.These results suggest a qualitative approach for utilizing RFLP markers to aid in selection of complex traits in commercial hybrid maize breeding programs. Commercial research programs produce thousands of crosses each year aimed at inbred line development. Discovery of molecular markers with consistent QTL associations across breeding populations and close QTL linkages would allow for rapid screening of new F2 populations at a few key markers. Early elimination of individuals with undesirable genotypes would reduce the extent of hybrid performance testing necessary during later stages of inbreeding. 相似文献
6.
A. Setiawan G. Koch S. R. Barnes C. Jung 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(8):1176-1182
The breeding of sugar beet varieties that combine resistance to Cercospora and high yield under non-diseased conditions is a major challenge to the breeder. The understanding of the quantitative trait
loci (QTLs) contributing to Cercospora resistance offers one route to solving this problem. A QTL analysis of Cercospora resistance in sugar beet was carried out using a linkage map based on AFLP and RFLP markers. Two different screening methods
for Cercospora resistance (a field test at Copparo, Italy, under natural infection, and a newly-developed leaf disc test) were used to estimate
the level of Cercospora resistance; the correlation between scores from the field (at 162 days after sowing) and the leaf disc test was significant.
QTL analysis was based on F2 and F3 (half-sib family) generations derived from crosses between diploid single plants of 93164P (resistant to Cercospora leaf spot disease) and 95098P (susceptible). Four QTLs associated with Cercospora resistance (based on Lsmean data of the leaf disc test) on chromosomes III, IV, VII and IX were revealed using Composite
interval mapping. To produce populations segregating for leaf spot resistance as a single Mendelian factor, we selected for
plants heterozygous for only one of the QTLs (on chromosome IV or IX) but homozygous for the others.
Received: 1 September 1999 / Accepted 7 October 1999 相似文献
7.
Akio Ohyama Kenta Shirasawa Hiroshi Matsunaga Satomi Negoro Koji Miyatake Hirotaka Yamaguchi Tsukasa Nunome Hiroyoshi Iwata Hiroyuki Fukuoka Takeshi Hayashi 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2017,130(8):1601-1616
Key message
Using newly developed euchromatin-derived genomic SSR markers and a flexible Bayesian mapping method, 13 significant agricultural QTLs were identified in a segregating population derived from a four-way cross of tomato.Abstract
So far, many QTL mapping studies in tomato have been performed for progeny obtained from crosses between two genetically distant parents, e.g., domesticated tomatoes and wild relatives. However, QTL information of quantitative traits related to yield (e.g., flower or fruit number, and total or average weight of fruits) in such intercross populations would be of limited use for breeding commercial tomato cultivars because individuals in the populations have specific genetic backgrounds underlying extremely different phenotypes between the parents such as large fruit in domesticated tomatoes and small fruit in wild relatives, which may not be reflective of the genetic variation in tomato breeding populations. In this study, we constructed F2 population derived from a cross between two commercial F1 cultivars in tomato to extract QTL information practical for tomato breeding. This cross corresponded to a four-way cross, because the four parental lines of the two F1 cultivars were considered to be the founders. We developed 2510 new expressed sequence tag (EST)-based (euchromatin-derived) genomic SSR markers and selected 262 markers from these new SSR markers and publicly available SSR markers to construct a linkage map. QTL analysis for ten agricultural traits of tomato was performed based on the phenotypes and marker genotypes of F2 plants using a flexible Bayesian method. As results, 13 QTL regions were detected for six traits by the Bayesian method developed in this study.8.
R. Heller J. Schondelmaier G. Steinrücken C. Jung 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1996,92(8):991-997
Sugar beet (Beta vulgaris L.) is highly susceptible to the beet cyst nematode (Heterodera schachtii Schm.). Three resistance genes originating from the wild beets B. procumbens (Hs1
pro-1) and B. webbiana (Hs1
web-1, Hs2
web-7) have been transferred to sugar beet via species hybridization. We describe the genetic localization of the nematode resistance genes in four different sugar beet lines using segregating F2 populations and RFLP markers from our current sugar beet linkage map. The mapping studies yielded a surprising result. Although the four parental lines carrying the wild beet translocations were not related to each other, the four genes mapped to the same locus in sugar beet independent of the original translocation event. Close linkage (0–4.6 cM) was found with marker loci at one end of linkage group IV. In two populations, RFLP loci showed segregation distortion due to gametic selection. For the first time, the non-randomness of the translocation process promoting gene transfer from the wild beet to the sugar beet is demonstrated. The data suggest that the resistance genes were incorporated into the sugar beet chromosomes by non-allelic homologous recombination. The finding that the different resistance genes are allelic will have major implications on future attempts to breed sugar beet combining the different resistance genes. 相似文献
9.
W. Wicki M. Winzeler J. E. Schmid P. Stamp M. Messmer 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(7-8):1265-1272
Sixteen crosses between eight winter wheat cultivars were screened for resistance to Septoria nodorum leaf and glume blotch in the F1 and F4 generations using artificial inoculation in the field. The F1 of most crosses showed dominance for susceptibility on both ear and leaf. The effects of general combining ability were of
similar magnitude as the effects for specific combining ability. On the basis of the phenotypic difference of the parents,
no prediction was possible about the amount and the direction of genetic variance in the segregating populations. The variation
observed in this study both within and among the segregating populations suggests a quantitative inheritance pattern influencing
the expression of the two traits. The components of variance between F2 families within a population were as high as (for S. nodorum blotch on the ear) or higher (for S. nodorum blotch on the leaf) than those between populations. Therefore, strong selection within a few populations may be as effective
to obtain new resistant genotypes as selection in a large number of populations. In almost all crosses, progenies were found
that were more resistant than the better parent. Thus transgression breeding may be a tool to breed for higher levels of resistance
to S. nodorum blotch. Highly resistant genotypes were found even in combination with two susceptible parents. The genetic source for Septoria resistance is probably broader than is generally assumed and could be used to improve S. nodorum resistance by combination breeding followed by strong selection in large populations.
Received: 18 January / Accepted: 30 April 1999 相似文献
10.
Taguchi K Ogata N Kubo T Kawasaki S Mikami T 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,118(2):227-234
Aphanomyces root rot, caused by Aphanomyces cochlioides Drechs., is one of the most serious diseases of sugar beet (Beta vulgaris L.). Identification and characterization of resistance genes is a major task in sugar beet breeding. To ensure the effectiveness
of marker-assisted screening for Aphanomyces root rot resistance, genetic analysis of mature plants’ phenotypic and molecular
markers’ segregation was carried out. At a highly infested field site, some 187 F2 and 66 F3 individuals, derived from a cross between lines ‘NK-310mm-O’ (highly resistant) and ‘NK-184mm-O’ (susceptible), were tested,
over two seasons, for their level of resistance to Aphanomyces root rot. This resistance was classified into six categories
according to the extent and intensity of whole plant symptoms. Simultaneously, two selected RAPD and 159 ‘NK-310mm-O’-coupled
AFLP were used in the construction of a linkage map of 695.7 cM. Each of nine resultant linkage groups was successfully anchored
to one of nine sugar beet chromosomes by incorporating 16 STS markers. Combining data for phenotype and molecular marker segregation,
a single QTL was identified on chromosome III. This QTL explained 20% of the variance in F2 population (in the year 2002) and 65% in F3 lines (2003), indicating that this QTL plays a major role in the Aphanomyces root rot resistance. This is the first report
of the genetic mapping of resistance to Aphanomyces-caused diseases in sugar beet. 相似文献
11.
Mirjam M. J. Jacobs Ben Vosman Vivianne G. A. A. Vleeshouwers Richard G. F. Visser Betty Henken Ronald G. van den Berg 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2010,120(4):785-796
Mapping resistance genes is usually accomplished by phenotyping a segregating population for the resistance trait and genotyping
it using a large number of markers. Most resistance genes are of the NBS-LRR type, of which an increasing number is sequenced.
These genes and their analogs (RGAs) are often organized in clusters. Clusters tend to be rather homogenous, viz. containing
genes that show high sequence similarity with each other. From many of these clusters the map position is known. In this study
we present and test a novel method to quickly identify to which cluster a new resistance gene belongs and to produce markers
that can be used for introgression breeding. We used NBS profiling to identify markers in bulked DNA samples prepared from
resistant and susceptible genotypes of small segregating populations. Markers co-segregating with resistance can be tested
on individual plants and directly used for breeding. To identify the resistance gene cluster a gene belongs to, the fragments
were sequenced and the sequences analyzed using bioinformatics tools. Putative map positions arising from this analysis were
validated using markers mapped in the segregating population. The versatility of the approach is demonstrated with a number
of populations derived from wild Solanum species segregating for P. infestans resistance. Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively. 相似文献
12.
Genetic analysis of male fertility restoration in wild cytoplasmic male sterility<Emphasis Type="Italic"> G</Emphasis> of beet 总被引:3,自引:0,他引:3
Touzet P Hueber N Bürkholz A Barnes S Cuguen J 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,109(1):240-247
Cytoplasmic male sterility (CMS) has been used in the breeding of sugar beet for decades but is also more generally an important feature of the reproductive system in its wild relative, Beta vulgaris ssp. maritima. Among the several CMSs found in wild populations, the G CMS is a mitochondrial variant of the respiratory chain. The segregants derived from a cross between a restored plant and a female (male-sterile) plant on G cytoplasm exhibited three sexual phenotypic classes: female, hermaphrodite and intermediate. The pattern of segregation suggests a genetic inheritance with two loci in epistatic interaction. Nevertheless, it was possible to apply a bulk segregant analysis approach to search for AFLP and microsatellite markers linked to the restorer locus (RfG1) which controls the capacity to produce pollen [female versus non female (i.e. intermediates and hermaphrodites)] in the segregating population. A linkage group was constructed with four AFLP markers and nine microsatellites, and a total size of 40 cM (Kosambi). The closest marker, a microsatellite, was totally linked to RfG1, which was also flanked by two AFLP markers delimiting a 5 cM window. This linkage group was identified as being chromosome VIII where neither of the restorer loci of the Owen CMS are located.Communicated by H.C. Becker 相似文献
13.
Xin Li Bevan Buirchell Guijun Yan Huaan Yang 《Molecular breeding : new strategies in plant improvement》2012,29(2):361-370
To broaden the gene pool of domesticated commercial cultivars of narrow-leafed lupin (Lupinus angustifolius L.), wild accessions are used as parents in crossing in lupin breeding. Among the progenies from wild × domesticated (W × D)
crosses, the soft-seediness gene mollis is the most difficult domestication gene to be selected by conventional breeding methods, where molecular marker-assisted
selection (MAS) is highly desirable. MAS in plant breeding requires markers to be cost-effective and high-throughput, and
be applicable to a wide range of crosses in a breeding program. In this study, representative plants from an F8 recombinant
inbred line (RIL) population derived from a W × D cross, together with four cultivars and four wild types, were used in DNA
fingerprinting by microsatellite-anchored fragment length polymorphisms (MFLP). Two co-dominant MFLP polymorphisms were identified
as candidate markers linked to the mollis gene, and one of the candidate markers was selected and converted into a co-dominant, sequence-specific PCR marker. This
marker, designated MoLi, showed a perfect match with phenotypes of seed coat permeability on a segregating population consisting
of 115 F8 RILs, confirming the close genetic linkage to the mollis gene. Validation tests showed that the banding pattern of marker MoLi is consistent with all the 25 historical and current
commercial cultivars released in Australia, and is consistent with mollis genotypes in 119 of the 125 accessions in the Australian L. angustifolius core collection. Marker MoLi provides a cost-effective way to select the mollis gene in a wide range of W × D crosses in lupin breeding. 相似文献
14.
Carolina Font i Forcada Nnadozie Oraguzie Ernesto Igartua María Ángeles Moreno Yolanda Gogorcena 《Tree Genetics & Genomes》2013,9(2):331-349
Marker–trait associations based on populations from controlled crosses have been established in peach using markers mapped on the peach consensus map. In this study, we explored the utility of unstructured populations for association mapping to determine useful marker–trait associations in peach/nectarine cultivars. We used 94 peach cultivars representing local Spanish and modern cultivars from international breeding programs that are maintained at the Experimental Station of Aula Dei, Spain. This collection was characterized for pomological traits and was screened with 40 SSR markers that span the peach genome. Population structure analysis using STRUCTURE software identified two subpopulations, the local and modern cultivars, with admixture within both groups. The local Spanish cultivars were somewhat less diverse than modern cultivars. Marker–trait associations were determined in TASSEL with and without modelling coefficient of membership (Q) values as covariates. The results showed significant associations with pomological traits. We chose three markers on LG4 because of their proximity to the endoPG locus (freestone–melting flesh) that strongly affects pomological traits. Two genotypes of BPPCT015 marker showed significant associations with harvest date, flavonoids and sorbitol. Also, two genotypes of CPPCT028 showed associations with harvest date, total phenolics, RAC, and total sugars. Finally, two genotypes of endoPG1 showed associations with flesh firmness and total sugars. The analysis of linkage disequilibrium (LD) revealed a high level of LD up to 20 cM, and decay at farther distances. Therefore, association mapping could be a powerful tool for identifying marker–trait associations and would be useful for marker-assisted selection in peach breeding. 相似文献
15.
In this study, genetic variability at codon 42 within prion protein (PRNP) gene and its associations with production traits were investigated in 2002 goats from four Chinese domestic breeds. The
frequencies of allele “A” ranged from 0.353 to 0.562 in analyzed goat breeds with Hardy–Weinberg equilibrium (P > 0.05) except Xinong Sannen (XNSN) dairy breed. The establishment of relationships between different genotypes and growth
traits was performed in Inner Mongolia white Cashmere (IMWC) breed and revealed an association of the polymorphism with body
weight at 7-year-old goats (P = 0.033). The individuals with genotype GG showed heavier body weight than those with genotype AA. Moreover, association
analysis detected two significant associations between different genotypes and cashmere yield and fiber length in IMWC breed
(P = 0.009, P = 0.048, respectively). In addition, three significant associations of different genotypes with density of milk (a.m. and
p.m.), solids-not-fat of milk (P = 0.013, P = 0.009 and P = 0.002), respectively, were found in XNSN breed. Genotype GG had better milk quality than others. These findings suggested
that the polymorphism of codon 42 within PRNP was a useful DNA marker for eliminating or selecting excellent individuals in relation to production traits in marker-assist
selection breeding of goat. 相似文献
16.
Saxena RK Cui X Thakur V Walter B Close TJ Varshney RK 《Functional & integrative genomics》2011,11(4):651-657
Single feature polymorphisms (SFPs) are microarray-based molecular markers that are detected by hybridization of DNA or cRNA
to oligonucleotide probes. With an objective to identify the potential polymorphic markers for drought tolerance in pigeonpea
[Cajanus cajan (L.) Millspaugh], an important legume crop for the semi-arid tropics but deficient in genomic resources, Affymetrix Genome
Arrays of soybean (Glycine max), a closely related species of pigeonpea were used on cRNA of six parental genotypes of three mapping populations of pigeonpea
segregating for agronomic traits like drought tolerance and pod borer (Helicoverpa armigiera) resistance. By using robustified projection pursuit method on 15 pair-wise comparisons for the six parental genotypes, 5,692
SFPs were identified. Number of SFPs varied from 780 (ICPL 8755 × ICPL 227) to 854 (ICPL 151 × ICPL 87) per parental combination
of the mapping populations. Randomly selected 179 SFPs were used for validation by Sanger sequencing and good quality sequence
data were obtained for 99 genes of which 75 genes showed sequence polymorphisms. While associating the sequence polymorphisms
with SFPs detected, true positives were observed for 52.6% SFPs detected. In terms of parental combinations of the mapping
populations, occurrence of true positives was 34.48% for ICPL 151 × ICPL 87, 41.86% for ICPL 8755 × ICPL 227, and 81.58% for
ICP 28 × ICPW 94. In addition, a set of 139 candidate genes that may be associated with drought tolerance has been identified
based on gene ontology analysis of the homologous pigeonpea genes to the soybean genes that detected SFPs between the parents
of the mapping populations segregating for drought tolerance. 相似文献
17.
QTL mapping by association analysis has recently gained interest in plant breeding research as an alternative to QTL mapping in segregating populations from biparental crosses. In a first experiment on whole-genome association analysis in rapeseed, 684 mapped AFLP markers were tested for association with 14 traits in a set of 84 canola quality winter rapeseed cultivars. For association analysis a general linear model was used. By testing significance of marker-trait associations against a false discovery rate of 0.2, between 1 and 34 associated markers were found for 10 of the 14 traits. Taking into account linkage disequilibrium between the significant markers, these markers represent between 1 and 22 putative QTL for the respective traits. The minimum phenotypic variance explained by the QTL for the different traits ranged from 15% to 53%. A subset of 27 markers were significantly associated with two or more traits. These markers were predominantly shared between traits that were significantly correlated at the phenotypic level. The results show clearly that in rapeseed, QTL mapping by association analysis is a viable alternative to QTL mapping in segregating populations. 相似文献
18.
Linghe Zeng William R. Meredith Jr. Osman A. Gutiérrez Deborah L. Boykin 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2009,119(1):93-103
Genetic improvement in yield and fiber quality is needed for worldwide cotton production. Identification of molecular markers
associated with fiber-related traits can facilitate selection for these traits in breeding. This study was designed to identify
associations between SSR markers and fiber traits using an exotic germplasm population, species polycross (SP), derived from
multiple crosses among Gossypium tetraploid species. The SP population underwent 11 generations of mixed random mating and selfing followed by 12 generations
of selfing. A total of 260 lines were evaluated for fiber-related traits under three environments in 2005 and 2006. Large
genotypic variance components in traits were identified relative to components of genotype × environment. Eighty-six primer
pairs amplified a total of 314 polymorphic fragments among 260 lines. A total of 202 fragments with above 6% allele frequency
were analyzed for associations. Fifty-nine markers were found to have a significant (P < 0.05, 0.01, or 0.001) association with six fiber traits. There were six groups identified within the population using structure
analysis. Allele frequency divergence among six groups ranged from 0.11 to 0.27. Of the 59 marker–trait associations, 39 remained
significant after correction for population structure and kinship using a mixed linear model. The effect of population sub-structure
on associations was most significant in boll weight among the traits analyzed. The sub-structure among the SP lines may be
caused by natural selection, the breeding method applied during development of inbred lines, and unknown factors. The identified
marker–trait associations can be useful in breeding and help determine genetic mechanisms underlying interrelationships among
fiber traits.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
19.
J. T. Eckard J. L. Gonzalez-Hernandez S. Chao P. St Amand G. Bai 《Molecular breeding : new strategies in plant improvement》2014,34(3):1281-1300
In plant species, construction of framework linkage maps to facilitate quantitative trait loci mapping and molecular breeding has been confined to experimental mapping populations. However, development and evaluation of these populations is detached from breeding efforts for cultivar development. In this study, we demonstrate that dense and reliable linkage maps can be constructed using extant breeding populations derived from a large number of crosses, thus eliminating the need for extraneous population development. Using 565 segregating F1 progeny from 28 four-way cross breeding populations, a linkage map of the hexaploid wheat genome consisting of 3,785 single nucleotide polymorphism (SNP) loci and 22 simple sequence repeat loci was developed. Map estimation was facilitated by application of mapping algorithms for general pedigrees implemented in the software package CRI-MAP. The developed linkage maps showed high rank-order concordance with a SNP consensus map developed from seven mapping studies. Therefore, the linkage mapping methodology presented here represents a resource efficient approach for plant breeding programs that enables development of dense linkage maps “on the fly” to support molecular breeding efforts. 相似文献
20.
Ibrokhim Y. Abdurakhmonov Sukumar Saha Jonnie N. Jenkins Zabardast T. Buriev Shukhrat E. Shermatov Brain E. Scheffler Alan E. Pepper John Z. Yu Russell J. Kohel Abdusattor Abdukarimov 《Genetica》2009,136(3):401-417
Cotton is the world’s leading cash crop, but it lags behind other major crops for marker-assisted breeding due to limited
polymorphisms and a genetic bottleneck through historic domestication. This underlies a need for characterization, tagging,
and utilization of existing natural polymorphisms in cotton germplasm collections. Here we report genetic diversity, population
characteristics, the extent of linkage disequilibrium (LD), and association mapping of fiber quality traits using 202 microsatellite
marker primer pairs in 335 G. hirsutum germplasm grown in two diverse environments, Uzbekistan and Mexico. At the significance threshold (r
2 ≥ 0.1), a genome-wide average of LD extended up to genetic distance of 25 cM in assayed cotton variety accessions. Genome
wide LD at r
2 ≥ 0.2 was reduced to ~5–6 cM, providing evidence of the potential for association mapping of agronomically important traits
in cotton. Results suggest linkage, selection, inbreeding, population stratification, and genetic drift as the potential LD-generating
factors in cotton. In two environments, an average of ~20 SSR markers was associated with each main fiber quality traits using
a unified mixed liner model (MLM) incorporating population structure and kinship. These MLM-derived significant associations
were confirmed in general linear model and structured association test, accounting for population structure and permutation-based
multiple testing. Several common markers, showing the significant associations in both Uzbekistan and Mexican environments,
were determined. Between 7 and 43% of the MLM-derived significant associations were supported by a minimum Bayes factor at
‘moderate to strong’ and ‘strong to very strong’ evidence levels, suggesting their usefulness for marker-assisted breeding
programs and overall effectiveness of association mapping using cotton germplasm resources.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献