Source: UNIV OF SOUTHERN CALIFORNIA submitted to
MAPPING QTL FOR YIELD HETEROSIS IN THE PACIFIC OYSTER
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
NRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0199867
Grant No.
2003-35205-14419
Project No.
CALR-2004-03723
Proposal No.
2004-03723
Multistate No.
(N/A)
Program Code
43.0
Project Start Date
Mar 1, 2004
Project End Date
Feb 28, 2006
Grant Year
2004
Project Director
Hedgecock, D.
Recipient Organization
UNIV OF SOUTHERN CALIFORNIA
(N/A)
LOS ANGELES,CA 90033
Performing Department
(N/A)
Non Technical Summary
Previously, we revealed striking heterosis or hybrid vigor in yield (viability and growth) of Pacific oysters and illuminated some of its genetic and physiological causes. The genetic and physiological bases of hybrid vigor have remained elusive for nearly a century, even in corn and other major crops for which hybrid vigor is the basis of improvement. The purpose of this project is to map regions of the genome contributing to the variation of growth and to determine how genes act to make hybrids superior. In addition to shedding light on the genetic mechanisms behind hybrid vigor, QTL maps should provide useful markers to assist in crossbreeding of oysters and validation of the contributions to yield of candidate genes that have been identified through an independent analysis of expression profiles in inbred and hybrid oysters. Much of the work was completed prior to transferring the project from the University of California, Davis, to the University of Southern California, including the development of AFLP markers, moderately dense linkage maps, and the collecting of individual growth histories in three, large, F2 mapping families. The work remaining to be accomplished is simply to genotype samples from these individually tagged F2 families and to carry out the appropriate statistical analyses of the data. Already we have determined that males and females differ in growth rate, so we are focusing efforts on two F2 families, whose sex was unambiguously determined by microscopic examination of gonad biopsy at the end of the growth period.
Animal Health Component
(N/A)
Research Effort Categories
Basic
80%
Applied
20%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
3033723108030%
3043723108060%
3053723108010%
Knowledge Area
305 - Animal Physiological Processes; 303 - Genetic Improvement of Animals; 304 - Animal Genome;

Subject Of Investigation
3723 - Oysters;

Field Of Science
1080 - Genetics;
Goals / Objectives
The primary objective of this project is to map quantitative trait loci (QTL) for yield heterosis and its components (survival and growth) in the Pacific oyster, using F2 populations and linkage maps of microsatellite DNA and AFLP markers. In support of this primary objective, we aim to develop microsatellite DNA and AFLP markers for use in linkage mapping and to construct moderately dense linkage maps for F2 mapping populations.
Project Methods
We are analyzing and mapping growth rate variation in F2 families made from the high-yielding F1 hybrids generated in 2001. In August 2002, we made replicate full-sib crosses of F1 parents to produce F2 mapping families. Seed were reared in both indoor and outdoor environments, although mapping is focusing on the outdoor-reared seed. For each of three families, we randomly selected and tagged 500 individuals, which were then re-deployed to the field in June 2003 and re-weighed monthly through October, yielding a 5-point growth curve for each individual. We previously completed low-density genetic linkage maps for male and female parents, which cover an estimated 75% to 80% of the genome. In order to increase the density of the linkage map for QTL mapping, we are developing and adding AFLP markers to the framework map made with microsatellite DNA markers. The male map now has 189 markers in 10 linkage groups, while the female map has 216 markers in 11 linkage groups. These new maps are estimated to cover 94% and 78% of the genome, respectively. Various statistical procedures for mapping growth rate variation onto these linkage maps are being employed.

Progress 03/01/04 to 02/28/06

Outputs
The project addressed and affirmed the null hypothesis that quantitative trait loci (QTL) for yield heterosis and its components (survival and growth) could be mapped in the Pacific oyster. The first linkage map was constructed for the Pacific oyster, using more than 100 microsatellite DNA markers, most of which were cloned in this and a previous NRI project. For the QTL mapping, we used F2 populations, particularly the 35x51 F2 family for which live weights of 500 individually tagged oysters were recorded monthly through their second growing season in 2004. In these F2 families, we expected classical Mendelian 1:2:1 segregation ratios of AA, AB, and BB genotypes at markers and QTL. The linkage map for this particular F2 family comprised 52 microsatellite DNA markers, in 11 linkage groups, covering 437 centimorgans (map units). Distortions of Mendelian ratios were observed for multiple markers on linkage groups (LG) II, IV, V, IX, and for single markers on LG Ia, III, VII, and VIII. These distortions resulted largely from selection against recessive deleterious mutations, as described by Launey & Hedgecock (2001 Genetics 159:255), producing, over all markers, moderate excesses of heterozygotes (frequency of AB = 0.53) and deficiencies of homozygotes (frequency of AA=0.22, frequency of BB=0.20). Upon harvest in October 2004, the mapping family was still in reproductive condition, so that sex could be determined by microscopic examination of gonadal smears. As seen previously, females were heavier than males, averaging 21.1 vs. 14.8 g live weight. Sex accounted for 20% of size variance at harvest and was subsequently included as a co-factor in mapping of growth QTL. We also mapped sex as a binary trait, which revealed major QTL on LG III, VIII, and IX. Our main goal was to map QTL for growth in an F2 family and to estimate their effects, i.e. given our interest in the genetic basis of hybrid vigor, we wished to know whether AB heterozygotes at QTL were superior to both the AA and BB homozygotes in growth (overdominant effect) or whether AB heterozygotes were only as good as the best homozygote (dominant effect). These two types of gene effect represent competing theories of hybrid vigor. We used both raw monthly live weight data, as well as derived measures such as growth rate between intervals and the inflection point between the exponential and asymptotic phases of fitted logistic growth models. We detected a major QTL affecting initial live weight and date of the inflection point in the growth curve on LG IV; this QTL showed near-complete dominance and explained over 40% of trait variance. For first live weight, another QTL located on LG VIII gave a rare signal of overdominance or heterozygote superiority. For final weight, we found a dominant QTL on LG IX, in about the same location as a QTL for the inflection point in logistic growth and for mid-summer growth rate. Most QTL effects support the dominance theory of hybrid vigor. We opportunistically mapped a recessive mutation causing abnormal shell shape and an additive factor affecting shell pigmentation; both traits are economically important characters.

Impacts
Discovering the genetic basis of hybrid vigor in the Pacific oyster sheds light on a phenomenon that has remained an enigma for a century, despite its global importance in crop improvement. Having detected markers that are linked to genes affecting growth and yield of the Pacific oyster, which has the highest annual production of any freshwater or marine organism, we have paved the way for using markers to increase the efficiency of commercial breeding programs. More importantly, we have provided a set of tools and procedures that enables future research aimed at uncovering the physiological mechanisms underlying hybrid vigor. The mapping methods and materials developed in this project permit validation of the quantitative effects of candidate genes being discovered through alternative genomic technologies, such as gene expression profiling, thus providing an important check on functional significance.

Publications

  • Bucklin, K. A. 2002. Genetic Load in Two Generations of the Pacific Oyster Crassostrea gigas. Ph.D. dissertation, genetics, University of California, Davis.
  • Hedgecock, D. 2003. Genomic approaches to understanding heterosis and improving yield in the Pacific oyster. In Aquatic Genomics, Shimizu, N., T. Aoki, I. Hirono, and F. Takashima (editors). Springer-Verlag, Tokyo. pp.73-83.
  • Li, G., S. Hubert, K. Bucklin, V. Ribes, and D. Hedgecock. 2003. Characterization of 79 microsatellite DNA markers in the Pacific oyster Crassostrea gigas. Molecular Ecology Notes 3:228-232.
  • Hubert, S., and D. Hedgecock. 2004. Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas. Genetics 168:351-362.
  • Hedgecock, D., G. Li, S. Hubert, K. Bucklin, and V. Ribes. 2004. Widespread null alleles and poor cross-species amplification of microsatellite DNA loci cloned from the Pacific oyster (Crassostrea gigas). Journal of Shellfish Research 23:379-385.
  • Hedgecock, D., P. M. Gaffney, P. Goulletquer, X. Guo, K. Reece, and G. W. Warr. 2005. The case for sequencing the Pacific oyster genome. Journal of Shellfish Research 24:429-441.
  • Yamtich, J., M.-L. Voigt, G. Li, and D. Hedgecock. 2005. Eight microsatellite loci for the Pacific oyster Crassostrea gigas. Animal Genetics 36:524-526.