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1.
More on the efficiency of marker-assisted selection 总被引:26,自引:0,他引:26
Frédéric Hospital L. Moreau F. Lacoudre A. Charcosset A. Gallais 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(8):1181-1189
Computer simulations were used to study the efficiency of marker-assisted selection (MAS) based on an index combining the
phenotypic value and the molecular score of individuals. The molecular score is computed from the effects attributed to markers
by multiple regression of phenotype on marker genotype. The results show that in the first generation the ratio RE of the
expected efficiency of MAS over the expected efficiency of purely phenotypic selection generally increases when considering:
(1) larger population sizes, (2) lower heritability values of the trait, and (3) a higher type-I error risk of the regression.
This is consistent with previously published results. However, at low heritabilities our results point out that response to
MAS is more variable than response to phenotypic selection. Hence, when the difference of genetic gains is considered instead
of their ratio, RE, the heritability values corresponding to maximal advantage of using MAS rather than phenotypic selection
are still low, but higher than predicted based on RE. The study over several successive generations of the rate of fixation
of QTLs shows that the higher efficiency of MAS on QTLs with large effects in early generations is balanced by a higher rate
of fixation of unfavourable alleles at QTLs with small effects in later generations. This explains why MAS may become less
efficient than phenotypic selection in the long term. MAS efficiency therefore depends on the genetic determinism of the trait.
Finally, we investigate a modified MAS method involving an alternation of selection on markers with and without phenotypic
evaluation. Our results indicate that such a selection method could at low cost, provide an important increase in the genetic
gain per unit of time in practical breeding programs.
Received: 11 July 1997 / Accepted: 4 August 1997 相似文献
2.
Fan Z Robbins MD Staub JE 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2006,112(5):843-855
Cucumber (Cucumis sativus L.; 2n=2x=14) has a narrow genetic base, and commercial yield of US processing cucumber has plateaued in the last 15 years. Yield may
be increased by altering plant architecture to produce unique early flowering (days to flower, DTF), female (gynoecious, GYN),
highly branched (multiple lateral branching, MLB), long-fruited (length:diameter ratio, L:D) cultivars with diverse plant
statures. The genetic map position of QTL conditioning these quantitatively inherited yield component traits is known, and
linked molecular markers may have utility in marker-assisted selection (MAS) programs to increase selection efficiency, and
effectiveness. Therefore, a base population (C0), created by intermating four unique but complementary lines, was subjected to three cycles (C1–C3) of phenotypic (PHE) mass selection for DTF, GYN, MLB, and L:D. In tandem, two cycles of marker-assisted backcrossing for
these traits began with selected C2 progeny (C2S) to produce families (F1[i.e., C2S × C2S], and BC1 [i.e., F1 × C2S]) for line extraction, and for comparative analysis of gain from selection by PHE selection, and MAS. Frequencies of marker
loci were used to monitor selection-dependent changes during PHE selection, and MAS. Similar gain from selection was detected
as a result of PHE selection, and MAS for MLB (~0.3 branches/cycle), and L:D (~0.1 unit increase/cycle) with concomitant changes
in frequency at linked marker loci. Although genetic gain was not realized for GYN during PHE selection, the percentage of
female flowers of plants subjected to MAS was increased (5.6–9.8% per cycle) depending upon the BC1 population examined. Selection-dependent changes in frequency were also detected at marker loci linked to female sex expression
during MAS. MAS operated to fix favorable alleles that were not exploited by PHE selection in this population, indicating
that MAS could be applied for altering plant architecture in cucumber to improve its yield potential.
The cost of publishing this paper was defrayed in part by the payment of page charges. Under postal regulations, this paper
therefore must be hereby, marked advertisement solely to indicate this fact. Mention of a trade name, proprietary product,
or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply its approval to the exclusion
of other products that may be suitable. 相似文献
3.
We examined gene models for two traits with and without antagonistic pleiotropy using a locus-based simulation model to investigate
the effects of different population sizes, heritabilities and economic weights, using index selection, and index selection
with optimum selection (OS), over 10 generations. Gene models included additive and dominance gene action, with equal and
varying initial allele frequencies with and without pleiotropy for a fixed level of resources (i.e. founder sizes each generation
of 40, 80 and 160 with progeny arrays that totaled 800 per generation). Pleiotropy (with an initial r
g of −0.5), reduced gain by ~8–10% when heritabilities for both traits were the same (0.2), relative to non-pleiotropic cases.
When traits had different heritabilities (i.e. 0.2 and 0.4), gains in the lower heritability trait were substantially lower,
especially with pleiotropy present. In general, OS with slightly larger population sizes could offset losses in gain, but
rarely overrode the large effects of different heritabilities or economic weights. Pleiotropy increased response variance
among traits, which was magnified when heritabilities were different. Identifying an appropriate weight on relatedness in
the OS process is important to manage coancestry expectations around the loss of alleles (or fixation of recessive alleles)
and to minimise response variance. The dynamics of selection intensity, drift, rate of coancestry build-up, response variance,
etc. are complex for multi-trait selection; however, a few economically viable strategies could reduce the adverse effects
of selecting against genetic correlations without drastically impairing gain. 相似文献
4.
R. Bernardo 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,98(3-4):551-556
Marker-based assortative mating (MAM) – the mating of individuals that have similar genotypes at random marker loci – can
increase selection response for a single trait by 3–8% over random mating (RM). Genetic gain is usually desired for multiple
traits rather than for a single trait. My objectives in this study were to (1) compare MAM, phenotypic assortative mating
(PAM), and RM of selected individuals for improving two traits and (2) determine when MAM will be most useful for improving
two traits. I simulated 20 generations of selecting 32 out of 200 individuals in an F2 population. The individuals were selected based on an index (SI) of two traits and were intermated by MAM, PAM, or RM. I
studied eight genetic models that differed in three contrasts: (1) weight, number of quantitative trait loci (QTL), and heritability
(h
2) for each trait; (2) linkage of QTL for each trait; and (3) trait means of the inbred parents of the F2. For SI and the two component traits, MAM increased short-term selection response by 5–8% in six out of the eight genetic
models. The MAM procedure was least effective in two genetic models, wherein the QTL for one trait were unlinked to the QTL
for the other trait and the parents of the F2 had divergent means for each trait. The loss of QTL heterozygosity was much greater with MAM than with PAM or RM. Consequently,
the advantage of MAM over RM dissipated after 5–7 generations. Differences were small between selection responses with PAM
and RM. The MAM procedure can enhance short-term selection response for two traits when selection is not stringent, h
2 is low, and the means of the parents of the F2 are equal for each trait.
Received: 10 June 1998 / Accepted: 5 August 1998 相似文献
5.
Fukino N Ohara T Monforte AJ Sugiyama M Sakata Y Kunihisa M Matsumoto S 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2008,118(1):165-175
Powdery mildew caused by Podosphaera xanthii is an important foliar disease in melon. To find molecular markers for marker-assisted selection, we constructed a genetic
linkage map of melon based on a population of 93 recombinant inbred lines derived from crosses between highly resistant AR
5 and susceptible ‘Earl’s Favourite (Harukei 3)’. The map spans 877 cM and consists of 167 markers, comprising 157 simple
sequence repeats (SSRs), 7 sequence characterized amplified region/cleavage amplified polymorphic sequence markers and 3 phenotypic
markers segregating into 20 linkage groups. Among them, 37 SSRs and 6 other markers were common to previous maps. Quantitative
trait locus (QTL) analysis identified two loci for resistance to powdery mildew. The effects of these QTLs varied depending
on strain and plant stage. The percentage of phenotypic variance explained for resistance to the pxA strain was similar between
QTLs (R
2 = 22–28%). For resistance to pxB strain, the QTL on linkage group (LG) XII was responsible for much more of the variance
(41–46%) than that on LG IIA (12–13%). The QTL on LG IIA was located between two SSR markers. Using an independent population,
we demonstrated the effectiveness of these markers. This is the first report of universal and effective markers linked to
a gene for powdery mildew resistance in melon. 相似文献
6.
Evaluation of marker-assisted selection through computer simulation 总被引:20,自引:0,他引:20
M. D. Edwards N. J. Page 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1994,88(3-4):376-382
Computer simulation was used to evaluate responses to marker-assisted selection (MAS) and to compare MAS responses with those typical of phenotypic recurrent selection (PRS) in an allogamous annual crop species such as maize (Zea mays L.). Relative to PRS, MAS produced rapid responses early in the selection process; however, the rate of these responses diminished greatly within three to five cycles. The gains from MAS ranged from 44.7 to 99.5% of the maximum potential, depending on the genetic model considered. Linkage distance between markers and quantitative trait loci (QTLs) was the factor which most limited the responses from MAS. When averaged across all models considered, flanking QTLs within two marker loci produced 38% more gain than did selection based on single markers if markers were loosely-linked to a QTL (20% recombination). Flanking markers were much less advantageous when markers were closely-linked to a QTL (5% recombination), producing an advantage over single markers of only 11%. Markers were most effective in fully exploiting the genetic potential when fewer QTLs controlled the trait. Large QTL numbers exacerbated the problem of marker-QTL recombination by requiring more generations for fixation. In annual crop species, MAS may offer a primary advantage of enabling two selection cycles per year versus the 2 years per cycle required by most PRS schemes for the evaluation of testcross progeny. MAS thus appears to allow very rapid gains for the first 2–3 years of recurrent selection, after which time conventional methods might replace MAS to achieve further responses.Publication number 19, 330 of the Minnesota Agricultural Experiment Station 相似文献
7.
M. C. Moretzsohn C. D. M. Nunes M. E. Ferreira D. Grattapaglia 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(1):63-70
Shell thickness is an important trait in oil palm breeding programs and is the basis for the classification of the varieties
of oil palm into the types dura, tenera and pisifera. This trait seems to be controlled by a single locus, with two alleles
(sh
+ and sh
−) showing codominant expression. Two single-tree linkage maps were constructed for a maternal tenera (sh
+
sh
−) palm and for a paternal pisifera (sh
−
sh
−) palm using the pseudo-testcross mapping strategy in combination with RAPD markers through the analysis of an F1 tenera×pisifera progeny. A total of 308 arbitrary primers were screened in a sample of eight F1 plants and 121 markers were detected in a testcross configuration. An average of 1.66 polymorphic marker per selected primer
were identified in this cross. At LOD 5.0 (with some few exceptions) and θ=0.25 the maternal tenera map included a total of
48 markers distributed in 12 linkage groups or pairs of markers (449.3 cM) while the paternal pisifera map included 42 markers
distributed in 15 linkage groups or pairs of markers (399.7 cM). We used RAPD and bulked segregant analysis (BSA) to identify
markers more tightly linked to the sh
+ locus. A total of 174 new primers not previously used in the linkage analysis were screened using bulks of DNA extracted
from plants selected for the contrasting shell-thickness phenotypes. Two RAPD markers (R11–1282 and T19–1046) were identified
to be linked on both sides of the sh
+ locus on linkage group 4. The estimated map distances from sh
+ to R11–1282 and to T19–1046 were 17.5 cM and 23.9 cM, respectively. The results demonstrate the usefulness of RAPD markers
and the pseudo-testcross mapping strategy for developing genetic linkage information, and constitute an important step towards
early marker-assisted selection for shell thickness in oil palm.
Received: 21 February 1999 / Accepted: 29 April 1999 相似文献
8.
Zhao Y Gowda M Liu W Würschum T Maurer HP Longin FH Ranc N Reif JC 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2012,124(4):769-776
Genomic selection is a promising breeding strategy for rapid improvement of complex traits. The objective of our study was
to investigate the prediction accuracy of genomic breeding values through cross validation. The study was based on experimental
data of six segregating populations from a half-diallel mating design with 788 testcross progenies from an elite maize breeding
program. The plants were intensively phenotyped in multi-location field trials and fingerprinted with 960 SNP markers. We
used random regression best linear unbiased prediction in combination with fivefold cross validation. The prediction accuracy
across populations was higher for grain moisture (0.90) than for grain yield (0.58). The accuracy of genomic selection realized
for grain yield corresponds to the precision of phenotyping at unreplicated field trials in 3–4 locations. As for maize up
to three generations are feasible per year, selection gain per unit time is high and, consequently, genomic selection holds
great promise for maize breeding programs. 相似文献
9.
Genomic selection in forest tree breeding 总被引:2,自引:0,他引:2
Genomic selection (GS) involves selection decisions based on genomic breeding values estimated as the sum of the effects of
genome-wide markers capturing most quantitative trait loci (QTL) for the target trait(s). GS is revolutionizing breeding practice
in domestic animals. The same approach and concepts can be readily applied to forest tree breeding where long generation times
and late expressing complex traits are also a challenge. GS in forest trees would have additional advantages: large training
populations can be easily assembled and accurately phenotyped for several traits, and the extent of linkage disequilibrium
(LD) can be high in elite populations with small effective population size (N
e) frequently used in advanced forest tree breeding programs. Deterministic equations were used to assess the impact of LD
(modeled by N
e and intermarker distance), the size of the training set, trait heritability, and the number of QTL on the predicted accuracy
of GS. Results indicate that GS has the potential to radically improve the efficiency of tree breeding. The benchmark accuracy
of conventional BLUP selection is reached by GS even at a marker density ~2 markers/cM when N
e ≤ 30, while up to 20 markers/cM are necessary for larger N
e. Shortening the breeding cycle by 50% with GS provides an increase ≥100% in selection efficiency. With the rapid technological
advances and declining costs of genotyping, our cautiously optimistic outlook is that GS has great potential to accelerate
tree breeding. However, further simulation studies and proof-of-concept experiments of GS are needed before recommending it
for operational implementation. 相似文献
10.
Glyptemys insculpta is considered to be one of the most endangered freshwater turtles in North America. Here microsatellite markers were employed
to investigate the genetic variation and population structure of G. insculpta at Delaware Water Gap National Recreation Area (USA). Seven microsatellites revealed high allelic variation with 13–30 alleles
per locus. Observed and expected heterozygosities per locus ranged from 0.875–0.925 to 0.888–0.952, respectively. Pairwise
estimates of population structure (θ) ranged from 0.000–0.013 to θ estimated over all loci and aggregations was not significantly different from zero. Gene flow (Nm) was high and ranged from 19 migrants per generation to infinity in pairwise comparisons. No significant relationship between
geographic distance and genetic distance was detected. These data indicate that G. insculpta at DEWA represent a single, genetically diverse management unit for conservation. 相似文献
11.
Genomic selection (GS) can be a powerful technology in conifer breeding because conifers have long generation intervals, protracted
evaluation times, and high costs of breeding inputs. To elucidate the potential of GS for conifer breeding, we simulated 60-year
breeding programs in Cryptomeria japonica with and without GS. In conifers, the rapid decay of linkage disequilibrium (LD) can constitute a severe barrier to application
of GS. For overcoming that barrier, we proposed an idea to leverage a seed orchard system, which has been used commonly in
conifers, because some degree of LD exists in progenies derived from the limited number of elite trees in a seed orchard.
The base population used for simulations consisted of progenies from 25 elite trees. Results show that GS breeding (GSB) done
without model updating outperformed phenotypic selection breeding (PSB) during the first 30 years, but the genetic gain achieved
over the 60 years was smaller in GSB than in PSB. However, GSB with model updating outperformed PSB over the 60 years. The
genetic gain achieved over the 60 years of GSB with model updating was nearly twice that of PSB. Advantages of GSB over PSB
prevailed, even for a low heritability polygenic trait. The number of markers necessary for efficient GS was a realistic level
(e.g., one in every 1 cM), although higher marker density engendered higher accuracy of selection. These results suggest that
GS can be useful in C. japonica breeding. Updating of the prediction model was, however, indispensable for attaining the large genetic gain. 相似文献
12.
Selection plans in plant and animal breeding are driven by genetic evaluation. Recent developments suggest using massive genetic marker information, known as "genomic selection." There is little evidence of its performance, though. We empirically compared three strategies for selection: (1) use of pedigree and phenotypic information, (2) use of genomewide markers and phenotypic information, and (3) the combination of both. We analyzed four traits from a heterogeneous mouse population (http://gscan.well.ox.ac.uk/), including 1884 individuals and 10,946 SNP markers. We used linear mixed models, using extensions of association analysis. Cross-validation techniques were used, providing assumption-free estimates of predictive ability. Sampling of validation and training data sets was carried out across and within families, which allows comparing across- and within-family information. Use of genomewide genetic markers increased predictive ability up to 0.22 across families and up to 0.03 within families. The latter is not statistically significant. These values are roughly comparable to increases of up to 0.57 (across family) and 0.14 (within family) in accuracy of prediction of genetic value. In this data set, within-family information was more accurate than across-family information, and populational linkage disequilibrium was not a completely accurate source of information for genetic evaluation. This fact questions some applications of genomic selection. 相似文献
13.
E. W. Andersson L. Sánchez Rodríguez B. Andersson 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1999,99(1-2):73-80
Integer Linear Programming was used to maximize genetic gain from selection at a given level of relatedness. Variances and
breeding values for total height were available for 296 plus-trees of Pinus sylvestris which had been evaluated by open-pollinated progeny testing at a single test site in northern Sweden. Second-generation breeding
and selection scenarios for this breeding population were evaluated using simulated data derived deterministically from normal
distributions of estimated breeding values of progeny around mid-parent family means. The study considered two mating designs,
assortative and non-assortative single-pair mating, and two selection criteria, individual phenotype and performance of half-sib
progeny. Relatedness (group coancestry) was restricted to a level equivalent to that given by within-family selection of 2
trees per family from each of 25 families (the current standard in Sweden). Selection that allows the best-performing families
to contribute a greater number of progeny was superior, both when the breeding population size was limited to 50 individuals
and when it was allowed to be larger. The selected set giving the greatest average breeding value under restricted group coancestry
included the best individual from families that would have been rejected under application of standard within-family selection.
We made a comparison of the present value on retrieved gain between phenotypic selection and evaluation by progeny testing.
Received: 24 November 1998 / Accepted: 14 December 1998 相似文献
14.
Rai R Singh AK Singh BD Joshi AK Chand R Srivastava CP 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2011,123(5):803-813
Pea rust caused by Uromyces fabae (Pers.) de-Bary is a major problem in warm humid regions causing huge economic losses. A mapping population of 136 F6:7 recombinant inbred lines (RILs) derived from the cross between pea genotypes, HUVP 1 (susceptible) and FC 1 (resistant) was
evaluated in polyhouse as well as under field conditions during two consecutive years. Infection frequency (IF) and area under
disease progress curve (AUDPC) were used for evaluation of rust reaction of the RILs. A linkage map was constructed with 57
polymorphic loci selected from 148 simple sequence repeats (SSRs), 3 sequence tagged sites (STS), and 2 random amplified polymorphic
(RAPD) markers covering 634 cM of genetic distance on the seven linkage groups of pea with an average interval length of 11.3 cM.
Composite interval mapping (CIM) revealed one major (Qruf) and one minor (Qruf1) QTL for rust resistance on LGVII. The LOD (5.2–15.8) peak for Qruf was flanked by SSR markers, AA505 and AA446 (10.8 cM), explaining 22.2–42.4% and 23.5–58.8% of the total phenotypic variation
for IF and AUDPC, respectively. The minor QTL was environment-specific, and it was detected only in the polyhouse (LOD values
4.2 and 4.8). It was flanked by SSR markers, AD146 and AA416 (7.3 cM), and explained 11.2–12.4% of the total phenotypic variation.
The major QTL Qruf was consistently identified across all the four environments. Therefore, the SSR markers flanking Qruf would be useful for marker-assisted selection for pea rust (U. fabae) resistance. 相似文献
15.
Godfrey Asea Bindiganavile S. Vivek Patrick E. Lipps Richard C. Pratt 《Molecular breeding : new strategies in plant improvement》2012,29(2):515-527
Northern corn leaf blight (NCLB) caused by Exserohilum turcicum, gray leaf spot (GLS) caused by Cercospora zeae-maydis and maize streak caused by maize streak Mastrevirus (MSV) are the most destructive foliar diseases limiting maize production in sub-Saharan Africa. Most foliar diseases of maize
are managed using quantitative (partial) resistance, and previous studies have reported quantitative trait loci associated
with host resistance (rQTL). Our objective was to compare the genetic gain and costs resulting from phenotypic, genotypic,
and marker-assisted selection of partially inbred lines derived from many families for resistance to infection by three foliar
pathogens. We developed a population of 410 F2:3 families by crossing inbred line CML202 with a breeding line designated VP31.
These families were planted in nurseries inoculated separately with each pathogen. We conducted one cycle of early generation
pedigree selection using three different procedures, phenotypic, genotypic, and marker/phenotypic index, for improvement of
resistance to each pathogen. We used simple sequence repeat (SSR) markers flanking six target rQTL associated with partial
resistance. Broad- and narrow-sense heritability estimates were also obtained for the F2:3 families, and selected and non-selected
F2:4 families. Genetic gains resulting from the selection procedures were determined. Gene action of the candidate rQTL was
determined using orthogonal contrasts. Estimates of costs based on lower boundary values indicated that the cost of marker-based
selection was lower than that of phenotypic selection. Our results indicate that molecular markers linked to target rQTL can
facilitate pyramiding resistance to multiple diseases during early generation pedigree selection. 相似文献
16.
F. Wilde V. Korzun E. Ebmeyer H. H. Geiger T. Miedaner 《Molecular breeding : new strategies in plant improvement》2007,19(4):357-370
Fusarium head blight (FHB) is one of the most economically important wheat diseases, resulting in losses in grain yield and quality
as well as contamination with deoxynivalenol (DON). Cultivar Sumai 3 from China and its descendants as well as var. Frontana from Brazil have been identified as potent sources of resistance and subsequently mapped by molecular markers. The aim of
the present study was to compare phenotypic and marker-based selection in spring wheat. In a double cross, we combined two
donor-quantitative trat loci (QTL) alleles from CM82036 (Sumai 3/Thornbird) located on chromosomes 3B and 5A and one donor-QTL allele from var. Frontana on chromosome 3A with two high-yielding German spring wheat varieties. This initial population was selected phenotypically
by a two- (CP1) and three-step procedure (CP1+) and by independent marker-based analysis using one to three flanking markers per QTL (CM). To estimate selection gain, the
two phenotypically selected variants and the marker-selected variant as well as an unselected variant (C0) were inoculated
with FHB in the field at four locations in 2004. Between 26 and 135 progeny were tested from each variant. FHB severity and
DON content were significantly reduced by all selection variants. The highest total selection gain was obtained by the three-step
phenotypic selection for both traits, although marker-based selection for the two donor-QTL alleles from CM82036 proved to
be more powerful on an annual basis. The large range of variation for FHB resistance and, to a lesser extent, DON content
within the marker-based variant, however, shows that an additional phenotypic selection will enhance selection gain. 相似文献
17.
Samantha M. Wisely Rachel M. Santymire Travis M. Livieri Sara A. Mueting JoGayle Howard 《Conservation Genetics》2008,9(2):389-399
Population augmentation with translocated individuals has been shown to alleviate the effects of bottlenecks and drift. The
first step to determine whether restoration for genetic considerations is warranted is to genetically monitor reintroduced
populations and compare results to those from the source. To assess the need for genetic restoration, we evaluated genetic
diversity and structure of reintroduced (n = 3) and captive populations of the endangered black-footed ferret (Mustela nigripes). We measured genotypic changes among populations using seven microsatellite markers and compared phenotypic changes with
eight morphometric characters. Results indicated that for the population which rapidly grew post-reintroduction, genetic diversity
was equivalent to the captive, source population. When growth languished, only the population that was augmented yearly maintained
diversity. Without augmentation, allelic diversity declined precipitously and phenotypic changes were apparent. Ferrets from
the genetically depaupertate population had smaller limbs and smaller overall body size than ferrets from the two populations
with greater diversity. Population divergence (F
ST = 0.10 ± 0.01) was surprisingly high given the common source of populations. Thus, it appears that 5–10 years of isolation
resulted in both genotypic divergence and phenotypic changes to populations. We recommend translocation of 30–40 captive individuals
per annum to reintroduction sites which have not become established quickly. This approach will maximize the retention of
genetic diversity, yet maintain the beneficial effects of local adaptation without being swamped by immigration. 相似文献
18.
Milan Lstib?rek Kristyna Ivankov�� Jan Kadlec Jaroslav Kobliha Jaroslav Kl��p?t�� Yousry A. El-Kassaby 《Tree Genetics & Genomes》2011,7(5):1069-1078
We present a probabilistic model to minimize the fingerprinting effort associated with the implementation of the “breeding
without breeding” scheme under partial pedigree reconstruction. Our approach is directed at achieving a declared target population’s
minimum effective population size (N
e
), following the pedigree reconstruction and genotypic selection and is based on the graph theory algorithm. The primary advantage
of the proposed method is to reduce the cost associated with fingerprinting before the implementation of the pedigree reconstruction
for seed parent–offspring derived from breeding arboreta and production or natural populations. Stochastic simulation was
conducted to test the method’s efficiency assuming a simple polygenic model and a single trait. Hypothetical population consisted
of 30 parental trees that were paired at random (selfing excluded), resulting in 600 individuals (potential candidates for
forwards selection). The male parentage was assumed initially unknown. The model was used to estimate the minimum genotyping
sample size needed to reaching the prescribed N
e
. Results were compared with the known pedigree data. The model was successful in revealing the true relationship pattern
over the whole range of N
e
. Two to three offspring entered genotyping to meet the N
e
= 2 while 41 to 43 were required to satisfy the N
e
= 14. Importantly, genetic gain was affected at the lower limits of the genotyping effort. Doubling the number of parents
resulted in considerable reduction of the genotyping effort at higher N
e
values. 相似文献
19.
A set of microsatellite markers was developed for Clinostigma savoryanum, an endemic palm species distributed in the Bonin Islands. We obtained 233 sequences that were unique, containing microsatellites
from an enriched library. Twelve loci were screened for their feasibility to be used as high resolution genetic markers using
each 30 individuals from two insular populations, Haha-jima and Mukou-jima. They showed polymorphisms of two to eight alleles
per locus and expected heterozygosities of 0.124–0.789. There is no evidence for significant scoring error due to stuttering,
large allele dropout and null alleles at 95% confidence interval except for the presence of null alleles in CLS00-77 of Mukou-jima population. 相似文献
20.
Development of SNP-based CAPS and dCAPS markers in eight different genes involved in starch biosynthesis in rice 总被引:3,自引:0,他引:3
Gi-An Lee Hee-Jong Koh Hun-Ki Chung Anupam Dixit Jong-Wook Chung Kyung-Ho Ma Sok-Young Lee Jung-Ro Lee Gang-Seob Lee Jae-Gyun Gwag Tae-San Kim Yong-Jin Park 《Molecular breeding : new strategies in plant improvement》2009,24(1):93-101
Single nucleotide polymorphisms (SNPs), which are inexhaustible, highly stable, and simply detectable sequence polymorphisms,
can lead to phenotypic variations by affecting protein composition changes. Here, we report development of 25 new cleaved
amplified polymorphic sequence or derived cleaved amplified polymorphic sequence markers that have discrete band sizes in
relation to the SNP genotypes in eight putative gene regions. The average frequency of DNA polymorphisms was 1 per 175 bp
(SNPs, 1 per 217 bp; In/dels, 1 per 906 bp). In primary statistical analysis of each marker on 55 diverse rice accessions,
including different ecotypes, the mean value of the major allele frequency was 0.658 (0.509–0.927). The average polymorphism
information content was 0.326 (0.126–0.375). The mean value of the inbreeding coefficient (f) was 0.950 and was positive (heterozygote deficiency) at all loci, corresponding to the inbreeding system in rice. In cluster
analysis, all rice accessions clustered mainly into three groups according to the ecotypes. The association analysis showed
that the SNP of Granule-bound starch synthase I and ADP-glucose pyrophosphorylase small subunit (ADPase-S) genes were highly associated with apparent amylose content variation than the others. These new SNP markers may be useful
in genotyping rice germplasm, in marker-assisted selection for improving starch quality and content, and in linkage as well
as association studies.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献