Genetic analysis of foal and studbook traits in selection for racing performance in trotters

The objective of this thesis was to evaluate the usefulness of body measurements and functional and conformation traits of foals and studbook horses in the breeding programmes of Finnhorse and Standardbred. Thus, nongenetic effects, heritability and repeatability, and genetic correlations for foal and studbook traits were estimated. In addition, genetic parameters for trotting race performance and genetic correlations for foal and studbook traits with racing traits were assessed. Genetic response and accuracy were estimated using records of animal, half-sibs, and parents in selection scenarios for racing traits, for foal and racing traits, and for studbook and racing traits, and using records of animal, half-sibs, and parents for foal traits and racing traits of parents. Single racing time and annual earnings were the breeding objectives in the selection scenarios. High heritability estimates (0.50 to 0.80) indicated that most part of the variation for body measurements of foals and studbook horses is additive genetic. High genetic correlations (0.74 to 0.99) between body measurements of foals and studbook horses indicated that the traits are determined by the same additive genes at all ages. Low to moderate genetic correlations between body measurements and racing traits suggested that selection favours a larger body size at all ages. Heritability of conformation and functional traits in foals were low to moderate (0.08 to 0.46), being generally higher than studbook traits (0.06 to 0.21). Leg stances of Finnhorse foals, type, body conformation, and overall grade of foals, and leg quality of studbook Finnhorses were of moderate heritability. Genetic correlations among the traits were from low to moderate. Partially based on the previous study, there were less unfavourable genetic correlations among foal than studbook traits. Genetic correlations between the same traits in foals and studbook horses were relatively high (over 0.60), indicating that scant new information would be received through studbook traits in genetic evaluation. In addition, the foal traits of type, trot, and overall grade were moderately to highly genetically correlated (0.50 to 0.70) with several studbook traits. Being mainly favourable for the breeding objective, genetic correlations for conformation and functional traits with racing traits were highest for the foal traits of type, trot, and overall grade and for the studbook traits of character and movements (0.37 to 0.90). Conformation traits in Finnhorse mainly had low genetic correlations with racing traits, whereas in Standardbred leg quality of studbook horses, body conformation, leg stances, and hooves of foals and studbook horses had moderate to high genetic correlations with several racing traits. The foal trait of walk is of little value in genetic evaluation of trotters due to a low heritability and low or unfavourable genetic correlations with racing traits. The most effective way to make genetic progress for the breeding objective is direct selection for racing time and earnings. No more than the individual records of one racing year are necessary for reasonable accuracy if the average number of racing records from different information sources is available for selection. The conformation and functional traits in foals are useful in genetic evaluation because they are less pre-selected than the traits in studbook horses, which are mostly determined by selection based on racing records. The most beneficial for the breeding objective is to use the foal traits of moderate heritability and genetic correlations with racing traits (type, trot, overall grade) in selection before a racing career in the index with racing records of relatives. The greatest gain in this scenario is due to a shorter generation interval. It is possible to implement for AI stallions. Functional and conformation traits in foals would also benefit from multi-trait selection in terms of prediction accuracy in the combined index with racing traits. The use of multivariate models for whole trait sets in estimation of covariance components would further correct for selection, resulting in more accurate estimates of genetic correlations than in this study. Investigating the economic value of foal traits and their relationship with veterinary records would elucidate the relevance of sound conformation and movements in breeding programmes. To have more effective conformation traits in selection for breeding programmes, judging based on biological variation for a specific trait using linear scores or all-or-none variables is recommended.Tutkimuksen tavoitteena oli arvioida varsojen ja kantakirjahevosten näyttelyominaisuuksien hyödyllisyys suomenhevosten ja lämminveristen ravihevosten jalostusohjelmissa, kun jalostustavoitteena on ravikilpailujen aika ja vuosittainen voittosumma. Näyttelyominaisuuksia ovat rungon mitat ja arvosteltavat rakenne-, luonne- ja liikeominaisuudet. Varsojen ja kantakirjahevosten näyttelyominaisuuksien perinnöllisyyden selvittäminen on tärkeää, koska niiden oletetaan olevan hyödyllisiä ravihevosen käyttökelpoisuuden ja kestävyyden jalostamisessa. Varsojen ja hevosten koko on hyvin periytyvää, sillä suurin osa eläinten välisistä eroista rungon mitoissa johtuu perinnöllisestä vaihtelusta. Rungon mittojen välillä on korkea perinnöllinen yhteys hevosen kaikissa ikävaiheissa ja jalostusvalinta ravimenestyksen suhteen suosii suurikokoisempia yksilöitä. Näyttelyissä arvosteltavat rakenne-, luonne- ja liikeominaisuudet ovat heikommin periytyviä kuin rungon mitat, sillä niiden periytyminen on alhaista tai kohtalaisen korkeaa. Varsojen arvosteltavat ominaisuudet ovat kuitenkin yleisesti paremmin periytyviä kuin kantakirjahevosten. Kohtalaisen korkeasti periytyviä arvosteltavia ominaisuuksia ovat jalkojen asento suomenhevosvarsoilla, varsan tyyppi, rungon rakenne ja näyttelypalkinto sekä jalkojen kovuus kantakirjasuomenhevosilla. Varsojen ja kantakirjahevosten vastaavilla ominaisuuksilla (rungon rakenne, jalka-asennot, kaviot ja raviliikkeet) on korkea perinnöllinen yhteys. Lisäksi varsan tyypin ja näyttelypalkinnon ja usean kantakirjaominaisuuden välillä on kohtalainen tai korkea perinnöllinen yhteys. Arvosteltavat ominaisuudet ovat suurimmaksi osaksi myönteisessä geneettisessä yhteydessä jalostustavoitteen kanssa. Korkeimmat geneettiset yhteydet ravikilpailutuloksiin arvioitiin varsojen tyypille, raviliikkeille ja näyttelypalkinnolle, ja kantakirjahevosten luonteelle ja liikkeille, mitkä vaihtelivat kohtalaisesta korkeaan. Suomenhevosten rakenneominaisuudet ovat enimmäkseen heikossa ja monet lämminveristen ravihevosten rakenneominaisuudet kohtalaisessa tai korkeassa perinnöllisessä yhteydessä ravikilpailumenestyksen kanssa. Molempien rotujen ravihevosvarsojen käynnin arvostelu näyttelyissä ei ole jalostuksellisesti hyödyllistä, koska käynnillä on alhainen periytyvyys, ja sen ja ravikilpailutulosten välinen geneettinen yhteys on lähellä nollaa tai jopa epäsuotuisa. Ravikilpailutulosten kohtalaisen korkean periytyvyyden ja toistuvuuden sekä keskenään korkeiden geneettisten yhteyksien seurauksena, yhden vuoden ravikilpailutulokset ovat riittävät arvosteluvarmuudelle jalostusindeksivalinnassa, kun keskimääräinen kilpailutulosmäärä on käytettävissä. Myönteisen perinnöllisen yhteyden ansiosta, ravikilpailumenestyksen jalostaminen edistää myös näyttelyissä arvosteltavia ominaisuuksia, vaikka niitä ei huomioitaisikaan valinnassa. Kaikki arvosteltavat ominaisuudet kuitenkin hyötyvät jalostusindeksivalinnasta ravikilpailutulosten kanssa arvosteluvarmuuden suhteen, koska ei-geneettiset tekijät kuten sukupuoli, ikä, vuodenaika, arvosteluvuosi ja hevosjalostusliitto vaikuttavat suuresti rakenne-, luonne- ja liikeominaisuuksiin. Varsojen rakenne- ja liikeominaisuudet ovat hyödyllisempiä jalostukselle kuin kantakirjahevosten vastaavat ominaisuudet, koska perinnölliset erot varsojen välillä ovat suurempia ja ympäristön vaihtelu pienempää kuin kantakirjahevosilla. Jalostusarvostelussa ravikilpailutulokset ja aineiston valikoituneisuus vaikuttavat enemmän kantakirjahevosten kuin varsojen ominaisuuksiin. Kantakirjaominaisuudet on mahdollista korvata varsanäyttelyiden ominaisuuksilla, koska nämä ominaisuudet ovat suurelta osin geneettisesti samoja ja sen vuoksi vain vähän uutta tietoa saadaan kantakirjanäyttelyissä arvosteltavien ominaisuuksien kautta. Jalostukselle suurin hyöty näyttelyissä arvosteltavista ominaisuuksista saadaan käyttämällä eläimen ja sen sukulaisten varsanäyttelyominaisuuksia sekä sukulaisten ravikilpailutuloksia jalostusindeksivalinnassa ennen omaa kilpailu-uraa, mikä on lyhyen sukupolven välisen ajan ansiota. Tämä valintaskenaario on mahdollista toteuttaa nuorilla keinosiemennysjalostukseen käytettävillä oriilla. Jalostusvalinnalle tehokkaampien rakenneominaisuuksien luomiseksi on suositeltavaa kehittää yksityiskohtaiset arvostelukohteet, jotka perustuvat ominaisuuksien biologiseen vaihteluun käyttäen lineaarista tai joko-tai arvostelumallia. Tulevaisuudessa ravihevosen kestävän rakenteen ja liikkeiden jalostusta voi tutkia arvioimalla näyttelyominaisuuksien taloudellisia arvoja ja yhteyttä hevosen terveyteen

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris

Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive x additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS

Suomenhevosten rakenneominaisuuksien perinnölliset tunnusluvut ja yhteydet ravikilpailutuloksiin

Pro-gradu-työ : Helsingin yliopisto, 1997

Heritability of conformation traits and their relationships to racing performance in the Finnhorse trotter

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Estimates of non-genetic effects and genetic parameters for body measures and subjectively scored traits in Finnhorse trotters

v2009o

Genetic improvement of resistance to cyclaneusma needle cast in Pinus radiata

Progeny testing of resistance to needle loss caused by Cyclaneusma minus has been included in the needle disease resistance strategy of Pinus radiata in New Zealand since the late 1970s. Data on progeny trials, two in the North Island of New Zealand and one in Tasmania, Australia were available to estimate heritability, between trait genetic correlations and genotype by environment interaction. Resistance to cyclaneusma needle cast had moderate estimates of heritability (0.25 to 0.46) at all sites. Genetic correlations between the assessed traits indicated that selection for faster early growth, i.e. tree height at age four and diameter at breast height at age six favours trees that are prone to Cyclaneusma infection, whilst a favourable genetic association between resistance to cyclaneusma needle cast and productivity was evident at later assessment that was at age nine. No significant genotype by environment interaction was found for resistance to cyclaneusma needle cast, however, stability of genotypes across a wider range of environments and with a high genetic connectedness require more research. Considerable genetic improvement can be achieved for resistance to cyclaneusma needle cast and indirect selection for the trait should be pursued by selecting for productivity and culling susceptible genotypes from breeding.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Evaluation of forest tree breeding strategies based on partial pedigree reconstruction through simulations: Pinus pinaster and Eucalyptus nitens as case studies

Despite recent developments in molecular markers, most forest tree breeding programmes do not use them routinely. One way to integrate markers would be to use them for pedigree reconstruction after a simplified mating design through polymix or open-pollinated breeding. Thanks to the latest developments in the POPSIM simulator, various breeding strategies, including some based on paternity recovery, were evaluated with specified constraints on the level of diversity over breeding cycles. These simulations were carried out in two case studies: the French Pinus pinaster (Ait.) and the New Zealand Eucalyptus nitens (H. Dean & Maiden) Maiden breeding programmes. The Pinus pinaster case study produced lower genetic gain for the polymix breeding strategy with paternity recovery compared with double-pair mating or optimal-contribution strategies. However, the polymix breeding strategy could be of interest if the mating design is faster to complete. In the Eucalyptus nitens case study, pedigree recovery was shown to be a mandatory step to controlling the erosion of diversity over breeding cycles. In both cases, the strategies based on pedigree reconstruction were applicable with a limited level of genotyping. Finally, these simulations allow some general recommendations to be drawn to help breeders when designing a strategy for forest tree breeding.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Additional file 1: of Genotype × site × silviculture interactions in radiata pine: knowledge, working hypotheses and pointers for research§

Three tables listing known or postulated first-order interactions involving genotype, site and silviculture in radiata pine.  These show provisional information, and as such are offered as the framework for updating, through further collation of existing literature, fresh data analysis, and fresh experimental work. Table S1. Known or postulated genotype × site interactions in radiata pine, in terms of role and effects of site on expression of genotypic differences for specific tree variables (Carson 1989; Kumar and Burdon 2010).  Table S2. Known or postulated genotype × silviculture interactions in radiata pine, in terms of role and effects of silviculture on expression of genotypic differences for specific tree variables.  Table S3. Known or postulated silviculture × site interaction in radiata pine, in terms of how impacts of site factors on means and expression of differences for specific tree variables are affected by silviculture (lower stockings/heavier thinning regimes, or fertiliser use). (DOCX 33 kb

Phenotypes_for_publication

Phenotypic data and design terms used in the mixed mode