Genomic selection in sugar beet breeding populations.

Abstract:

BACKGROUND:Genomic selection exploits dense genome-wide marker data to predict breeding values. In this study we used a large sugar beet population of 924 lines representing different germplasm types present in breeding populations: unselected segregating families and diverse lines from more advanced stages of selection. All lines have been intensively phenotyped in multi-location field trials for six agronomically important traits and genotyped with 677 SNP markers. RESULTS:We used ridge regression best linear unbiased prediction in combination with fivefold cross-validation and obtained high prediction accuracies for all except one trait. In addition, we investigated whether a calibration developed based on a training population composed of diverse lines is suited to predict the phenotypic performance within families. Our results show that the prediction accuracy is lower than that obtained within the diverse set of lines, but comparable to that obtained by cross-validation within the respective families. CONCLUSIONS:The results presented in this study suggest that a training population derived from intensively phenotyped and genotyped diverse lines from a breeding program does hold potential to build up robust calibration models for genomic selection. Taken together, our results indicate that genomic selection is a valuable tool and can thus complement the genomics toolbox in sugar beet breeding.

journal_name

BMC Genet

journal_title

BMC genetics

authors

Würschum T,Reif JC,Kraft T,Janssen G,Zhao Y

doi

10.1186/1471-2156-14-85

subject

Has Abstract

pub_date

2013-09-18 00:00:00

pages

85

issn

1471-2156

pii

1471-2156-14-85

journal_volume

14

pub_type

杂志文章
  • LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs.

    abstract:BACKGROUND:Linkage disequilibrium (LD) mapping is commonly used to evaluate markers for genome-wide association studies. Most types of LD software focus strictly on LD analysis and visualization, but lack supporting services for genotyping. RESULTS:We developed a freeware called LD2SNPing, which provides a complete pa...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-10-26

    authors: Chang HW,Chuang LY,Chang YJ,Cheng YH,Hung YC,Chen HC,Yang CH

    更新日期:2009-06-06 00:00:00

  • Genomic and expression analysis of multiple Sry loci from a single Rattus norvegicus Y chromosome.

    abstract:BACKGROUND:Sry is a gene known to be essential for testis determination but is also transcribed in adult male tissues. The laboratory rat, Rattus norvegicus, has multiple Y chromosome copies of Sry while most mammals have only a single copy. DNA sequence comparisons with other rodents with multiple Sry copies are incon...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-8-11

    authors: Turner ME,Martin C,Martins AS,Dunmire J,Farkas J,Ely DL,Milsted A

    更新日期:2007-04-04 00:00:00

  • Fine-scale genetic analysis of the exploited Nile monitor (Varanus niloticus) in Sahelian Africa.

    abstract:BACKGROUND:Overexploitation of wildlife populations results in direct consequences, such as extinction and local extirpation, as well as indirect effects including genetic diversity loss and changes in genetic structure. A clear understanding of the underlying genetic patterns of harvested species is necessary for sust...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0188-x

    authors: Dowell SA,de Buffrénil V,Kolokotronis SO,Hekkala ER

    更新日期:2015-03-28 00:00:00

  • Genome-enabled predictions for binomial traits in sugar beet populations.

    abstract:BACKGROUND:Genomic information can be used to predict not only continuous but also categorical (e.g. binomial) traits. Several traits of interest in human medicine and agriculture present a discrete distribution of phenotypes (e.g. disease status). Root vigor in sugar beet (B. vulgaris) is an example of binomial trait ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-15-87

    authors: Biscarini F,Stevanato P,Broccanello C,Stella A,Saccomani M

    更新日期:2014-07-22 00:00:00

  • Comparative mapping combined with homology-based cloning of the rice genome reveals candidate genes for grain zinc and iron concentration in maize.

    abstract:BACKGROUND:Grain zinc and iron concentration is a complex trait that is controlled by quantitative trait loci (QTL) and is important for maintaining body health. Despite the substantial effort that has been put into identifying QTL for grain zinc and iron concentration, the integration of independent QTL is useful for ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-015-0176-1

    authors: Jin T,Chen J,Zhu L,Zhao Y,Guo J,Huang Y

    更新日期:2015-02-14 00:00:00

  • qDTY₁.₁, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds.

    abstract:BACKGROUND:Drought is one of the most important abiotic stresses causing drastic reductions in yield in rainfed rice environments. The suitability of grain yield (GY) under drought as a selection criterion has been reported in the past few years. Most of the quantitative trait loci (QTLs) for GY under drought in rice r...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-89

    authors: Vikram P,Swamy BP,Dixit S,Ahmed HU,Teresa Sta Cruz M,Singh AK,Kumar A

    更新日期:2011-10-18 00:00:00

  • Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms.

    abstract::Genome read categorization determines the genome of origin for sequence reads from an allopolyploid organism. Different techniques have been used to perform read categorization, mostly based on homoeo-SNPs identified between extant diploid relatives of allopolyploids. We present a novel technique for read categorizati...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-16-S2-S4

    authors: Page JT,Udall JA

    更新日期:2015-01-01 00:00:00

  • The association of the PON1 Q192R polymorphism with coronary heart disease: findings from the British Women's Heart and Health cohort study and a meta-analysis.

    abstract:BACKGROUND:There have been inconsistent results from case-control studies assessing the association of the PON1 Q192R polymorphism with coronary heart disease (CHD). Most studies have included predominantly men and the association in women is unclear. Since lipid levels vary between the sexes the antioxidant effect of ...

    journal_title:BMC genetics

    pub_type: 杂志文章,meta分析,评审

    doi:10.1186/1471-2156-5-17

    authors: Lawlor DA,Day IN,Gaunt TR,Hinks LJ,Briggs PJ,Kiessling M,Timpson N,Smith GD,Ebrahim S

    更新日期:2004-06-23 00:00:00

  • Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle.

    abstract:BACKGROUND:Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poor...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-15-15

    authors: Ogawa S,Matsuda H,Taniguchi Y,Watanabe T,Nishimura S,Sugimoto Y,Iwaisaki H

    更新日期:2014-02-03 00:00:00

  • Evidence for bivariate linkage of obesity and HDL-C levels in the Framingham Heart Study.

    abstract:BACKGROUND:Epidemiological studies have indicated that obesity and low high-density lipoprotein (HDL) levels are strong cardiovascular risk factors, and that these traits are inversely correlated. Despite the belief that these traits are correlated in part due to pleiotropy, knowledge on specific genes commonly affecti...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-4-S1-S52

    authors: Arya R,Lehman D,Hunt KJ,Schneider J,Almasy L,Blangero J,Stern MP,Duggirala R,Framingham Heart Study.

    更新日期:2003-12-31 00:00:00

  • Comparing self-reported ethnicity to genetic background measures in the context of the Multi-Ethnic Study of Atherosclerosis (MESA).

    abstract:BACKGROUND:Questions remain regarding the utility of self-reported ethnicity (SRE) in genetic and epidemiologic research. It is not clear whether conditioning on SRE provides adequate protection from inflated type I error rates due to population stratification and admixture. We address this question using data obtained...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-28

    authors: Divers J,Redden DT,Rice KM,Vaughan LK,Padilla MA,Allison DB,Bluemke DA,Young HJ,Arnett DK

    更新日期:2011-03-04 00:00:00

  • Mapping and validation of major quantitative trait loci for kernel length in wild barley (Hordeum vulgare ssp. spontaneum).

    abstract:BACKGROUND:Kernel length is an important target trait in barley (Hordeum vulgare L.) breeding programs. However, the number of known quantitative trait loci (QTLs) controlling kernel length is limited. In the present study, we aimed to identify major QTLs for kernel length, as well as putative candidate genes that migh...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-016-0438-6

    authors: Zhou H,Liu S,Liu Y,Liu Y,You J,Deng M,Ma J,Chen G,Wei Y,Liu C,Zheng Y

    更新日期:2016-09-13 00:00:00

  • Detecting responses to treatment with fenofibrate in pedigrees.

    abstract:BACKGROUND:Fenofibrate (Fb) is a known treatment for elevated triglyceride (TG) levels. The Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study was designed to investigate potential contributors to the effects of Fb on TG levels. Here, we summarize the analyses of 8 papers whose authors had access to the GO...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-018-0652-5

    authors: Cherlin S,Wang MH,Bickeböller H,Cantor RM

    更新日期:2018-09-17 00:00:00

  • A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

    abstract:BACKGROUND:Tyrosinemia type I, the most severe disease of the tyrosine catabolic pathway is caused by a deficiency in fumarylacetoacetate hydrolase (FAH). A patient showing few of the symptoms associated with the disease, was found to be a compound heterozygote for a splice mutation, IVS6-1g->t, and a putative missense...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-2-9

    authors: Dreumont N,Poudrier JA,Bergeron A,Levy HL,Baklouti F,Tanguay RM

    更新日期:2001-01-01 00:00:00

  • Meta-analysis of haplotype-association studies: comparison of methods and empirical evaluation of the literature.

    abstract:BACKGROUND:Meta-analysis is a popular methodology in several fields of medical research, including genetic association studies. However, the methods used for meta-analysis of association studies that report haplotypes have not been studied in detail. In this work, methods for performing meta-analysis of haplotype assoc...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-12-8

    authors: Bagos PG

    更新日期:2011-01-19 00:00:00

  • A genome-wide association study for harness racing success in the Norwegian-Swedish coldblooded trotter reveals genes for learning and energy metabolism.

    abstract:BACKGROUND:Although harness racing is of high economic importance to the global equine industry, significant genomic resources have yet to be applied to mapping harness racing success. To identify genomic regions associated with harness racing success, the current study performs genome-wide association analyses with th...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-018-0670-3

    authors: Velie BD,Fegraeus KJ,Solé M,Rosengren MK,Røed KH,Ihler CF,Strand E,Lindgren G

    更新日期:2018-08-29 00:00:00

  • GM and KM immunoglobulin allotypes in the Galician population: new insights into the peopling of the Iberian Peninsula.

    abstract:BACKGROUND:The current genetic structure of Iberian populations has presumably been affected by the complex orography of its territory, the different people and civilizations that settled there, its ancient and complex history, the diverse and persistent sociocultural patterns in its different regions, and also by the ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-8-37

    authors: Calderón R,Lodeiro R,Varela TA,Fariña J,Ambrosio B,Guitard E,González-Martín A,Dugoujon JM

    更新日期:2007-06-27 00:00:00

  • Identification and characterization of four Drosophila suzukii cellularization genes and their promoters.

    abstract:BACKGROUND:The spotted-wing Drosophila (Drosophila suzukii) is a widespread invasive pest that causes severe economic damage to fruit crops. The early development of D. suzukii is similar to that of other Drosophilids, but the roles of individual genes must be confirmed experimentally. Cellularization genes coordinate ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-020-00939-y

    authors: Yan Y,Jaffri SA,Schwirz J,Stein C,Schetelig MF

    更新日期:2020-12-18 00:00:00

  • Molecular and cytological analysis of widely-used Gal4 driver lines for Drosophila neurobiology.

    abstract:BACKGROUND:The Drosophila central nervous system (CNS) is a convenient model system for the study of the molecular mechanisms of conserved neurobiological processes. The manipulation of gene activity in specific cell types and subtypes of the Drosophila CNS is frequently achieved by employing the binary Gal4/UAS system...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-020-00895-7

    authors: Ogienko AA,Andreyeva EN,Omelina ES,Oshchepkova AL,Pindyurin AV

    更新日期:2020-10-22 00:00:00

  • Bayesian shrinkage mapping of quantitative trait loci in variance component models.

    abstract:BACKGROUND:In this article, I propose a model-selection-free method to map multiple quantitative trait loci (QTL) in variance component model, which is useful in outbred populations. The new method can estimate the variance of zero-effect QTL infinitely to zero, but nearly unbiased for non-zero-effect QTL. It is analog...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-11-30

    authors: Fang M

    更新日期:2010-04-29 00:00:00

  • Comparisons of methods for linkage analysis and haplotype reconstruction using extended pedigree data.

    abstract::We compare and contrast the performance of SIMPLE, a Monte Carlo based software, with that of several other methods for linkage and haplotype analyses, focusing on the simulated data from the New York City population. First, a whole-genome scan study based on the microsatellite markers was performed using GENEHUNTER. ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-6-S1-S76

    authors: Lin S,Ding J,Dong C,Liu Z,Ma ZJ,Wan S,Xu Y

    更新日期:2005-12-30 00:00:00

  • Precise single base substitution in the shibire gene by CRISPR/Cas9-mediated homology directed repair in Bactrocera tryoni.

    abstract:BACKGROUND:Pest eradication using the Sterile Insect Technique (SIT) involves high-density releases of sterilized males that mate with wild females and ultimately suppress the population. Sterilized females are not required for SIT and their removal or separation from males prior to release remains challenging. In orde...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-020-00934-3

    authors: Choo A,Fung E,Chen IY,Saint R,Crisp P,Baxter SW

    更新日期:2020-12-18 00:00:00

  • Genetic variation, population structure and linkage disequilibrium in peach commercial varieties.

    abstract:BACKGROUND:Peach [Prunus persica (L.) Batsch] is one of the most economically important fruit crops that, due to its genetic and biological characteristics (small genome size, taxonomic proximity to other important species and short juvenile period), has become a model plant in genomic studies of fruit trees. Our aim w...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-11-69

    authors: Aranzana MJ,Abbassi el-K,Howad W,Arús P

    更新日期:2010-07-20 00:00:00

  • Age-stratified heritability estimation in the Framingham Heart Study families.

    abstract::The Framingham Heart Study provides a unique source of longitudinal family data related to CVD risk factors. Age-stratified heritability estimates were obtained over three age groups (31-49 years, 50-60 years, and 61-79 years), reflecting the longitudinal nature of the data, for four quantitative traits. Age-adjusted ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-4-S1-S32

    authors: Brown WM,Beck SR,Lange EM,Davis CC,Kay CM,Langefeld CD,Rich SS,Framingham Heart Study.

    更新日期:2003-12-31 00:00:00

  • Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment length polymorphism (AFLP).

    abstract:BACKGROUND:Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 3...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-7-10

    authors: Laurentin HE,Karlovsky P

    更新日期:2006-02-16 00:00:00

  • MTH1 and RGT1 demonstrate combined haploinsufficiency in regulation of the hexose transporter genes in Saccharomyces cerevisiae.

    abstract:BACKGROUND:The SNF3 gene in the yeast Saccharomyces cerevisiae encodes a low glucose sensor that regulates expression of an important subset of the hexose transporter (HXT) superfamily. Null mutations of snf3 result in a defect in growth on low glucose concentrations due to the inability to relieve repression of a subs...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-13-107

    authors: Dietzel KL,Ramakrishnan V,Murphy EE,Bisson LF

    更新日期:2012-12-12 00:00:00

  • The challenge for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases.

    abstract::Genetic epidemiologists have taken the challenge to identify genetic polymorphisms involved in the development of diseases. Many have collected data on large numbers of genetic markers but are not familiar with available methods to assess their association with complex diseases. Statistical methods have been developed...

    journal_title:BMC genetics

    pub_type: 社论

    doi:10.1186/1471-2156-7-23

    authors: Heidema AG,Boer JM,Nagelkerke N,Mariman EC,van der A DL,Feskens EJ

    更新日期:2006-04-21 00:00:00

  • Genome-wide linkage analysis of congenital heart defects using MOD score analysis identifies two novel loci.

    abstract:BACKGROUND:Congenital heart defects (CHD) is the most common cause of death from a congenital structure abnormality in newborns and is often associated with fetal loss. There are many types of CHD. Human genetic studies have identified genes that are responsible for the inheritance of a particular type of CHD and for s...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-14-44

    authors: Flaquer A,Baumbach C,Piñero E,García Algas F,de la Fuente Sanchez MA,Rosell J,Toquero J,Alonso-Pulpon L,Garcia-Pavia P,Strauch K,Heine-Suñer D

    更新日期:2013-05-24 00:00:00

  • Quantitative trait loci for variation in immune response to a Foot-and-Mouth Disease virus peptide.

    abstract:BACKGROUND:Infectious disease of livestock continues to be a cause of substantial economic loss and has adverse welfare consequences in both the developing and developed world. New solutions to control disease are needed and research focused on the genetic loci determining variation in immune-related traits has the pot...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/1471-2156-11-107

    authors: Leach RJ,Craigmile SC,Knott SA,Williams JL,Glass EJ

    更新日期:2010-12-07 00:00:00

  • Molecular basis of a new ovine model for human 3M syndrome-2.

    abstract:BACKGROUND:Brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS, OMIA 001595-9940 ) is a previously reported recessively inherited disorder in Australian Poll Merino/Merino sheep. Affected lambs are stillborn with various congenital defects as reflected in the name of the disease, as well as short stature, ...

    journal_title:BMC genetics

    pub_type: 杂志文章

    doi:10.1186/s12863-020-00913-8

    authors: Woolley SA,Hayes SE,Shariflou MR,Nicholas FW,Willet CE,O'Rourke BA,Tammen I

    更新日期:2020-09-15 00:00:00