Effectiveness of selective genotyping for detection of quantitative trait loci: an analysis of grain and malt quality traits in three barley populations

Genetic dissection of grain architecture-related traits in a winter wheat population

BACKGROUND

The future productivity of wheat (T. aestivum L.) as the most grown crop worldwide is of utmost importance for global food security. Thousand kernel weight (TKW) in wheat is closely associated with grain architecture-related traits, e.g. kernel length (KL), kernel width (KW), kernel area (KA), kernel diameter ratio (KDR), and factor form density (FFD). Discovering the genetic architecture of natural variation in these traits, identifying QTL and candidate genes are the main aims of this study. Therefore, grain architecture-related traits in 261 worldwide winter accessions over three field-year experiments were evaluated.

RESULTS

Genome-wide association analysis using 90K SNP array in FarmCPU model revealed several interesting genomic regions including 17 significant SNPs passing false discovery rate threshold and strongly associated with the studied traits. Four of associated SNPs were physically located inside candidate genes within LD interval e.g. BobWhite_c5872_589 (602,710,399 bp) found to be inside TraesCS6A01G383800 (602,699,767-602,711,726 bp). Further analysis reveals the four novel candidate genes potentially involved in more than one grain architecture-related traits with a pleiotropic effects e.g. TraesCS6A01G383800 gene on 6A encoding oxidoreductase activity was associated with TKW and KA. The allelic variation at the associated SNPs showed significant differences betweeen the accessions carying the wild and mutated alleles e.g. accessions carying C allele of BobWhite_c5872_589, TraesCS6A01G383800 had significantly higher TKW than the accessions carying T allele. Interestingly, these genes were highly expressed in the grain-tissues, demonstrating their pivotal role in controlling the grain architecture.

CONCLUSIONS

These results are valuable for identifying regions associated with kernel weight and dimensions and potentially help breeders in improving kernel weight and architecture-related traits in order to increase wheat yield potential and end-use quality.

Assessing trait contribution and mapping novel QTL for salinity tolerance using the Bangladeshi rice landrace Capsule

BACKGROUND

Salinity is one of the most widespread abiotic stresses affecting rice productivity worldwide. The purpose of this study was to establish the relative importance of different traits associated with salinity tolerance in rice and to identify new quantitative trait loci (QTL) conferring tolerance to salinity at seedling stage. A total of 231 F_2:3 plants derived from a cross between a sensitive variety BRRI dhan29 (BR29 hereafter) and Capsule, a salt tolerant Bangladeshi indica landrace, were evaluated under salt stress in a phytotron.

RESULTS

Out of the 231 F₂ plants, 47 highly tolerant and 47 most sensitive lines were selected, representing the two extreme tails of the phenotypic distribution. These 94 plants were genotyped for 105 simple sequence repeat (SSR) and insertion/deletion (InDel) markers. A genetic linkage map spanning approximately 1442.9 cM of the 12 linkage groups with an average marker distance of 13.7 cM was constructed. QTL were identified on the long arm of chromosome 1 for Na⁺ concentration, K⁺ concentration, Na⁺-K⁺ ratio and survival; chromosome 3 for Na⁺ concentration, survival and overall phenotypic evaluation using the Standard Evaluation system (SES); and chromosome 5 for SES. A total of 6 pairwise epistatic interactions were also detected between QTL-linked and QTL-unlinked regions. Graphical genotyping indicated an association between the phenotypes of the extreme families and their QTL genotypes. Path coefficient analysis revealed that Na⁺ concentration, survival, Na⁺-K⁺ ratio and the overall phenotypic performance (SES score) are the major traits associated with salinity tolerance of Capsule.

CONCLUSIONS

Capsule provides an alternative source of salinity tolerance aside from Pokkali and Nona Bokra, the two Indian salt tolerant landraces traditionally used for breeding salt tolerant rice varieties. Pyramiding the new QTL identified in this study with previously discovered loci, such as Saltol, will facilitate breeding varieties that are highly tolerant of salt stress.

Identification and mapping of QTLs associated with drought tolerance traits in rice by a cross between Super Basmati and IR55419-04

Water stress, in a climate change scenario is one of the major threats for sustainable rice productivity. Combining drought resistance with yield and desirable economic traits is the most promising solution for the researchers. Although several studies resulted in the identification of QTLs for drought resistance in rice, but none of them serve as a milestone. Therefore, there is always a quest to find the new QTLs. The present investigation was carried out to map QTLs involved in drought resistance and yield related parameter in a cross of IR55419-04 and Super Basmati. An F₂ population of 418 individuals was used as the mapping population. The raised nursery was transplanted in lyzimeters. Two extreme sets of tolerant (23 Nos.) and sensitive (23 Nos.) individuals were selected based on total water uptake under water stress conditions. Two hundred thirty microsatellite markers staggered on the whole genome were used for identifying polymorphic markers between the two parents. The selected 73 polymorphic microsatellites were used to genotype individuals and were scattered on a distance of 1735 cM on all 12 linkage groups. QTL analysis was performed by using the WinQTL Cartographer 2.5 V. A total of 21 QTLs were detected using composite interval mapping. The QTLs relating to drought tolerance at the vegetative stage were found on chromosome 1. Novel genomic regions were detected in the marker interval RM520-RM143 and RM168-RM520. The region has a significant QTL qTWU3.1 for total water uptake. Root morphological trait QTLs were found on chromosome 3. QTLs responsible for additive effects were due to the alleles of the IR55419-04. These novel QTLs can be used for marker assisted breeding to develop new drought-tolerant rice varieties and fine mapping can be used to explore the functional relationship between the QTLs and phenotypic traits.

Multi-Population Selective Genotyping to Identify Soybean [Glycine max (L.) Merr.] Seed Protein and Oil QTLs

Plant breeders continually generate ever-higher yielding cultivars, but also want to improve seed constituent value, which is mainly protein and oil, in soybean [Glycine max (L.) Merr.]. Identification of genetic loci governing those two traits would facilitate that effort. Though genome-wide association offers one such approach, selective genotyping of multiple biparental populations offers a complementary alternative, and was evaluated here, using 48 F2:3 populations (n = ∼224 plants) created by mating 48 high protein germplasm accessions to cultivars of similar maturity, but with normal seed protein content. All F2:3 progeny were phenotyped for seed protein and oil, but only 22 high and 22 low extreme progeny in each F2:3 phenotypic distribution were genotyped with a 1536-SNP chip (ca 450 bimorphic SNPs detected per mating). A significant quantitative trait locus (QTL) on one or more chromosomes was detected for protein in 35 (73%), and for oil in 25 (52%), of the 48 matings, and these QTL exhibited additive effects of ≥ 4 g kg(-1) and R(2) values of 0.07 or more. These results demonstrated that a multiple-population selective genotyping strategy, when focused on matings between parental phenotype extremes, can be used successfully to identify germplasm accessions possessing large-effect QTL alleles. Such accessions would be of interest to breeders to serve as parental donors of those alleles in cultivar development programs, though 17 of the 48 accessions were not unique in terms of SNP genotype, indicating that diversity among high protein accessions in the germplasm collection is less than what might ordinarily be assumed.

The ABI4-induced Arabidopsis ANAC060 transcription factor attenuates ABA signaling and renders seedlings sugar insensitive when present in the nucleus

Seedling establishment is inhibited on media containing high levels (∼ 6%) of glucose or fructose. Genetic loci that overcome the inhibition of seedling growth on high sugar have been identified using natural variation analysis and mutant selection, providing insight into sugar signaling pathways. In this study, a quantitative trait locus (QTL) analysis was performed for seedling sensitivity to high sugar in a Col/C24 F2 population of Arabidopsis thaliana. A glucose and fructose-sensing QTL, GSQ11, was mapped through selective genotyping and confirmed in near-isogenic lines in both Col and C24 backgrounds. Allelism tests and transgenic complementation showed that GSQ11 lies within the ANAC060 gene. The Col ANAC060 allele confers sugar insensitivity and was dominant over the sugar-sensitive C24 allele. Genomic and mRNA analyses showed that a single-nucleotide polymorphism (SNP) in Col ANAC060 affects the splicing patterns of ANAC060 such that 20 additional nucleotides are present in the mRNA. The insertion created a stop codon, resulting in a truncated ANAC60 protein lacking the transmembrane domain (TMD) that is present in the C24 ANAC060 protein. The absence of the TMD results in the nuclear localization of ANAC060. The short version of the ANAC060 protein is found in ∼ 12% of natural Arabidopsis accessions. Glucose induces GSQ11/ANAC060 expression in a process that requires abscisic acid (ABA) signaling. Chromatin immunoprecipitation-qPCR and transient expression analysis showed that ABI4 directly binds to the GSQ11/ANAC060 promoter to activate transcription. Interestingly, Col ANAC060 reduced ABA sensitivity and Glc-induced ABA accumulation, and ABI4 expression was also reduced in Col ANAC060 lines. Thus, the sugar-ABA signaling cascade induces ANAC060 expression, but the truncated Col ANAC060 protein attenuates ABA induction and ABA signaling. This negative feedback from nuclear ANAC060 on ABA signaling results in sugar insensitivity.

Resistance to a rhabdovirus (VHSV) in rainbow trout: identification of a major QTL related to innate mechanisms

Health control is a major issue in animal breeding and a better knowledge of the genetic bases of resistance to diseases is needed in farm animals including fish. The detection of quantitative trait loci (QTL) will help uncovering the genetic architecture of important traits and understanding the mechanisms involved in resistance to pathogens. We report here the detection of QTL for resistance to Viral Haemorrhagic Septicaemia Virus (VHSV), a major threat for European aquaculture industry. Two induced mitogynogenetic doubled haploid F2 rainbow trout (Oncorhynchus mykiss) families were used. These families combined the genome of susceptible and resistant F0 breeders and contained only fully homozygous individuals. For phenotyping, fish survival after an immersion challenge with the virus was recorded, as well as in vitro virus replication on fin explants. A bidirectional selective genotyping strategy identified seven QTL associated to survival. One of those QTL was significant at the genome-wide level and largely explained both survival and viral replication in fin explants in the different families of the design (up to 65% and 49% of phenotypic variance explained respectively). These results evidence the key role of innate defence in resistance to the virus and pave the way for the identification of the gene(s) responsible for resistance. The identification of a major QTL also opens appealing perspectives for selective breeding of fish with improved resistance.

Marker-assisted selection for early-season cold tolerance in sorghum: QTL validation across populations and environments

Sorghum [Sorghum bicolor (L.) Moench] landraces from China generally exhibit excellent emergence and seedling vigor under cool conditions, and are being used as sources of genes for improvement of seedling cold tolerance in other cultivars. Marker-assisted selection (MAS) could expedite the introgression of genes from landraces into elite lines, however, only a few studies have empirically demonstrated efficacy of MAS for quantitatively inherited agronomic traits. In a preceding study we identified quantitative trait loci (QTL) for early-season performance in a recombinant inbred (RI) population, one parent of which was a cold-tolerant Chinese line, 'Shan Qui Red' (SQR). In this study, three SSR markers (Xtxp43, Xtxp51, and Xtxp211), each representing a QTL, were tested in two new populations: (Tx2794 x SQR F(3)) and (Wheatland x SQR BC(1)F(3)). Individual families were genotyped, and early-season field performance was measured for two years. Statistical analyses showed that the SQR allele of Xtxp43 had favorable effects on seedling vigor in both populations, and on emergence in the Tx2794 population. A large positive effect of the SQR allele of Xtxp51 was observed in the Tx2794 population for vigor and emergence. Slight genotype by environment interaction was observed for Xtxp51 in the Wheatland population. Marker Xtxp211 had small but significant effects on seedling vigor and emergence in both populations. Various interactions between loci were also significant. This study validated QTL markers in various genetic backgrounds, and demonstrated the utility of MAS for a quantitative trait, early-season cold tolerance, evaluated in the field.

Powdery mildew resistance in roses: QTL mapping in different environments using selective genotyping

Podosphaera pannosa, the causal agent of rose powdery mildew, hampers the production of cut roses throughout the world. A major tool to control this disease is the use of resistant plant material. Single resistance genes, like Rpp1, may be overcome within a few years by high risk pathogens like powdery mildews. Durable resistance could be achieved using quantitative resistances. Here we describe mapping of QTLs for resistance to P. pannosa in six different environments (artificial and natural infections in the greenhouse over 3 years and natural infections in the field over 2 years). AFLPs, RGAs and other marker types were used to construct an integrated linkage map for the diploid population 97/7 containing 233 markers. In a selective genotyping procedure, marker segregation was analysed for 170 of the up to 270 phenotyped individuals. We identified seven linkage groups with an average length of 60 cM, corresponding to seven rose chromosomes in the haploid set. Using an LOD significance threshold of 3.9 we detected a total of 28 QTLs for the nine powdery mildew disease scores under analysis. Using the data from artificial inoculations with powdery mildew race 9, three resistance QTLs explaining about 84% of the variability were mapped. Twelve and 15 QTLs were detected for resistance to naturally occurring infections in the greenhouse and in the field, respectively, over several years.

Mapping PrBn and other quantitative trait loci responsible for the control of homeologous chromosome pairing in oilseed rape (Brassica napus L.) haploids

In allopolyploid species, fair meiosis could be challenged by homeologous chromosome pairing and is usually achieved by the action of homeologous pairing suppressor genes. Oilseed rape (Brassica napus) haploids (AC, n=19) represent an attractive model for studying the mechanisms used by allopolyploids to ensure the diploid-like meiotic pairing pattern. In oilseed rape haploids, homeologous chromosome pairing at metaphase I was found to be genetically based and controlled by a major gene, PrBn, segregating in a background of polygenic variation. In this study, we have mapped PrBn within a 10-cM interval on the C genome linkage group DY15 and shown that PrBn displays incomplete penetrance or variable expressivity. We have identified three to six minor QTL/BTL that have slight additive effects on the amount of pairing at metaphase I but do not interact with PrBn. We have also detected a number of other loci that interact epistatically, notably with PrBn. Our results support the idea that, as in other polyploid species, metaphase I homeologous pairing in oilseed rape haploids is controlled by an integrated system of several genes, which function in a complex manner.

Genomic regions involved in response to grain yield selection at high and low nitrogen fertilization in maize

In order to validate the role of genomic regions involved in nitrogen use efficiency and detected in a population of recombinant inbred lines (RIL), we have applied from the same population a recurrent selection for adaptation to low N-input (N0) and to high N-input (N1). Variation of allele frequency at neutral marker during the two cycles of recurrent selection may provide information about markers linked to QTLs. Significant temporal variation of allele frequency was investigated using the test of Waples, which tests the hypothesis of genetic drift versus selection. Most genomic regions (12/19) responding to selection were detected for selection at high N-input and only two were common to selection at high and low N-inputs. This was consistent with the greater grain yield response to selection observed for the population selected under high N-input compared with the population selected under low N-input, when they were evaluated at high N-fertilization. In contrast, when they were evaluated at low N-input both types of selection gave similar yield. As was expected, in the first cycle we observed selection of markers linked to grain yield QTLs. In the course of the second cycle three situations were observed: the confirmation of most regions already selected in C1 including all C1 regions overlapping with grain yield QTLs; the non-confirmation of some C1 regions (2/9); and the identification of new genomic zones (10/17). The detected marker-QTL associations revealed the consistency of the involvement of some traits, such as root architecture and glutamine synthetase activity, which would be of major importance for grain yield setting whatever the nitrogen fertilization.

QTL analysis of Fusarium head blight resistance using a high-density linkage map in barley

Fusarium head blight (FHB) resistance was evaluated in a set of recombinant inbred (RI) lines from a cross between Russia 6 (resistant) and H.E.S. 4 (susceptible), which had one of the widest differences of FHB resistance reactions among ca. 5,000 barley germplasm accessions in Okayama University. Field-grown spikes were sampled and inoculated by the 'cut-spike test'. Resistance reactions on the parents and RI lines were scored by eleven grades, from resistant (0) to susceptible (10). Quantitative trait loci (QTL) analysis detected three QTL: two located on the long arm of chromosome 2H, and another on the short arm of chromosome 5H. A QTL located on chromosome 2H was coincident with the vrs1 locus, which governs inflorescence row type. The other QTL on chromosome 2H was positioned in the vicinity of cleistogamy locus (cly1 or Cly2) that determines inflorescence opening/closing. Resistant gene analog (RGA) and expressed sequence tag (EST) markers with homology for disease resistance genes were integrated into the high-density linkage map. Most of these markers were not localized near the identified resistance QTL, except for one RGA marker (FXLRRfor_XLRRrev170) localized in the vicinity of the cly1/Cly2 locus. Five AFLP markers localized in the vicinity of the identified QTL were sequenced to convert them into sequence tagged site (STS) markers. Genotyping of each RI line using two AFLP-STS markers and the vrs1 locus indicated that the RI lines with three Russia 6 QTL alleles exhibited the same level of high FHB resistance reactions as Russia 6. In contrast, RI lines with three susceptible alleles showed reactions close to H.E.S. 4. Therefore, the markers closely linked to the QTL can be efficiently used for the selection of resistance.

Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust

The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-resampling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.

Identification and validation of QTL for Sclerotinia midstalk rot resistance in sunflower by selective genotyping

Midstalk rot, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in sunflower (Helianthus annuus L.). Objectives of this study were to: (1) estimate the number, genomic positions and genetic effects of quantitative trait loci (QTL) for resistance to midstalk rot in line TUB-5-3234, derived from an interspecific cross; (2) determine congruency of QTL between this line and other sources of resistance; and (3) make inferences about the efficiency of selective genotyping (SG) in detecting QTL conferring midstalk rot resistance in sunflower. Phenotypic data for three resistance (stem lesion, leaf lesion and speed of fungal growth) and two morphological (leaf length and leaf length with petiole) traits were obtained from 434 F3 families from cross CM625 (susceptible) x TUB-5-3234 (resistant) under artificial infection in field experiments across two environments. The SG was applied by choosing the 60 most resistant and the 60 most susceptible F3 families for stem lesion. For genotyping of the respective F2 plants, 78 simple sequence repeat markers were used. Genotypic variances were highly significant for all traits. Heritabilities and genotypic correlations between reMidstalk rot, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in sunflower (Helianthus annuus L.). Objectives of this study were to: (1) estimate the number, genomic positions and genetic effects of quantitative trait loci (QTL) for resistance to midstalk rot in line TUB-5-3234, derived from an interspecific cross; (2) determine congruency of QTL between this line and other sources of resistance; and (3) make inferences about the efficiency of selective genotyping (SG) in detecting QTL conferring midstalk rot resistance in sunflower. Phenotypic data for three resistance (stem lesion, leaf lesion and speed of fungal growth) and two morphological (leaf length and leaf length with petiole) traits were obtained from 434 F3 families from cross CM625 (susceptible) x TUB-5-3234 (resistant) under artificial infection in field experiments across two environments. The SG was applied by choosing the 60 most resistant and the 60 most susceptible F3 families for stem lesion. For genotyping of the respective F2 plants, 78 simple sequence repeat markers were used. Genotypic variances were highly significant for all traits. Heritabilities and genotypic correlations between resistance traits were moderate to high. Three to four putative QTL were detected for each resistance trait explaining between 40.8% and 72.7% of the genotypic variance (PTS). Two QTL for stem lesion showed large genetic effects and corroborated earlier findings from the cross NDBLOSsel (resistant) x CM625 (susceptible). Our results suggest that SG can be efficiently used for QTL detection and the analysis of congruency for resistance genes across populations.

Fine mapping of a grain-weight quantitative trait locus in the pericentromeric region of rice chromosome 3

As the basis for fine mapping of a grain-weight QTL, gw3.1, a set of near isogenic lines (NILs), was developed from an Oryza sativa, cv. Jefferson x O. rufipogon (IRGC105491) population based on five generations of backcrossing and seven generations of selfing. Despite the use of an interspecific cross for mapping and the pericentromeric location of the QTL, we observed no suppression of recombination and have been able to narrow down the location of the gene underlying this QTL to a 93.8-kb region. The locus was associated with transgressive variation for grain size and grain weight in this population and features prominently in many other inter- and intraspecific crosses of rice. The phenotype was difficult to evaluate due to the large amount of variance in size and weight among grains on a panicle and between grains on primary and secondary panicles, underscoring the value of using multiple approaches to phenotyping, including extreme sampling and NIL group-mean comparisons. The fact that a QTL for kernel size has also been identified in a homeologous region of maize chromosome 1 suggests that this locus, in which the dominant O. rufipogon allele confers small seed size, may be associated with domestication in cereals.

Selection bias in quantitative trait loci mapping

A simulation study was performed to see whether selection affected quantitative trait loci (QTL) mapping. Populations under random selection, under selection among full-sib families, and under selection within a full-sib family were simulated each with heritability of 0.3, 0.5, and 0.7. They were analyzed with the marker spacing of 10 cM and 20 cM. The accuracy for QTL detection decreased for the populations under selection within full-sib family. Estimates of QTL effects and positions differed (P < .05) from their input values. The problems could be ignored when mapping a QTL for the populations under selection among full-sib families. A large heritability helped reduction of such problems. When the animals were selected within a full-sib family, the QTL was detected for the populations with heritability of 0.5 or larger using the marker spacing of 10 cM, and with heritability of 0.7 using the marker spacing of 20 cM. This study implied that when selection was introduced, the accuracy for QTL detection decreased and the estimates of QTL effects were biased. A caution was warranted on the decision of data (including selected animals to be genotyped) for QTL mapping.

Exploiting selective genotyping to study genetic diversity of resistance to Fusarium head blight in barley

Numerous barley cultivars from around the world have been identified as potential sources of Fusarium head blight (FHB) resistance genes. All of these cultivars exhibit partial resistance, and several mapping studies have shown that resistance to FHB is controlled by multiple genes. Successful development of barley cultivars with high levels of FHB resistance will require combining genes from multiple sources. We characterized five potential new sources of FHB resistance ('AC Oxbow', 'Atahualpa', 'HOR211', 'PFC88209', and 'Zhedar#1') to determine if they contain new FHB resistance genes. Cluster analysis, using a set of 80 SSR markers distributed throughout the genome, showed that most of the new sources of resistance were not similar to three cultivars that have been used in previous FHB mapping studies ('Chevron', 'Frederickson', and 'Gobernadora'), with 'Atahualpa' and 'HOR211' being the most dissimilar. By selective genotyping, we determined whether markers linked to six known FHB resistance quantitative trait loci (QTLs), discovered in other genotypes, explained variation for resistance in advanced breeding populations created from the new sources of resistance. Markers linked to four of the six known QTLs were associated with FHB severity in at least one of the populations. However, none of the six QTL regions were associated with variation for FHB severity in populations derived from crosses that utilized sources of resistance HOR211 or PFC88209. Selective genotyping is an efficient method for breeders to utilize current QTL information about disease resistance to search for new resistance genes.

An association study using AFLP markers and application to a beef cattle breeding population

Using amplified fragment length polymorphism (AFLP) fingerprinting, selective genotyping was performed to determine if this method was effective for selecting superior breeding stock. Forty-eight cows with extreme genetic merit for beef marbling score (BMS) were selected from a population of Japanese Black cattle (n = 4462), including 25 with the highest for predicted breeding value (PBV) and 23 with the lowest. Sixteen AFLP fragments were selected for further analysis based on fragment frequency differences between the high and low groups. A linear discriminant analysis using these AFLP fragments was applied in order to derive a discriminant function that classified the cows into high and low groups. Seven of the 16 fragments were included in the resulting function and the discriminant scores (general genetic values, GGV) of the 48 cows were calculated using the function. These cows were clearly separated into high and low groups by GGV with a correlation ratio of 0.91 (discriminative error of 2.1%). The same function was then applied to 121 additional cows that were randomly selected from the original population. A significant regression coefficient of GGV on BMS-PBV (R2 = 0.45) was obtained, which indicates that the GGV can be used as a selection criterion for BMS in this population. These results suggest that AFLP fingerprinting can be used for animal breeding without identifying the underlying genes affecting the trait of interest.