Fine-scale estimation of outcrossing in western redcedar with microsatellite assay of bulked DNA

Genetic architecture of terpene chemistry and growth traits and the impact of inbreeding on these traits in western redcedar ( Thuja plicata )

Western redcedar (WRC; Thuja plicata) is a conifer of the Pacific Northwest of North America prized for its durable and rot-resistant wood. WRC has naturally low outcrossing rates and readily self-fertilizes in nature. Challenges faced in WRC breeding and propagation involve selecting trees for accelerated growth while also ensuring enhanced heartwood rot resistance and resistance to ungulate browsing, as well as mitigating potential effects of inbreeding depression. Terpenes, a large and diverse class of specialized metabolites, confer both rot and browse resistance in the wood and foliage of WRC, respectively. Using a Bayesian modelling approach, we isolated single nucleotide polymorphism (SNP) markers estimated to be associated with three different foliar terpene traits and four different heartwood terpene traits, as well as two growth traits. We found that all traits were complex, being associated with between 1700 and 3600 SNPs linked with putatively causal loci, with significant polygenic components. Growth traits tended to have a larger polygenic component while terpene traits had larger major gene components; SNPs with small or polygenic effect were spread across the genome, while larger-effect SNPs tended to be localized to specific linkage groups. To determine whether there was inbreeding depression for terpene chemistry or growth traits, we used mixed linear models for a genomic selection training population to estimate the effect of the inbreeding coefficient F on foliar terpenes, heartwood terpenes and several growth and dendrochronological traits. We did not find significant inbreeding depression for any assessed trait. We further assessed inbreeding depression across four generations of complete selfing and found that not only was inbreeding depression not significant but that selection for height growth was the only significant predictor for growth during selfing, suggesting that inbreeding depression due to selfing during operational breeding can be mitigated by increased selection intensity.

Inbreeding in Chinese Fir: Insight into the Rare Self-Fertilizing Event from a Genetic View

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a fast-growing conifer with great forestation value and prefers outcrossing with high inbreeding depression effect. Previously, we captured a special Chinese fir parent clone named as 'cx569' that lacks early inbreeding depression. In view of the fact that very little has been published about the rare self-fertilizing event in Chinese fir from a genetic view, herein, we conduct an SSR-based study on the variation of open- and self-pollinated offspring of this parent to gain a view of the rare self-fertilizing event. The results indicated that genetic diversity of self-pollinated offspring was significantly reduced by half (Ho: 0.302, vs. 0.595, p = 0.001; He: 0.274 vs. 0.512, p = 0.002) when compared to an open-pollinated set. Self-pollinated offspring also had significantly positive FIS values (FIS = 0.057, p = 0.034) with a much higher proportion of common allele (20.59% vs. 0), reflecting their heterozygote deficiency. Clustering analysis further indicated a separation of the self- and opened- pollinated groups, implying a natural preference of outcrossing for cx569. However, the cx569 still had 6% acceptance for selfing. When accepted 100% for its own pollen, the cx569 led to a genetically unique selfing group. Additionally, this selfing group seemed to be consistently homozygous at seven particular loci. These findings gave us more genetic clues to gain insight into the rare self-fertilizing event in conifer (Chinese fir).

Genomic selection reveals hidden relatedness and increased breeding efficiency in western redcedar polycross breeding

Western redcedar (WRC) is an ecologically and economically important forest tree species characterized by low genetic diversity with high self-compatibility and high heartwood durability. Using sequence capture genotyping of target genic and non-genic regions, we genotyped 44 parent trees and 1520 offspring trees representing 26 polycross (PX) families collected from three progeny test sites using 45,378 SNPs. Trees were phenotyped for eight traits related to growth, heartwood and foliar chemistry associated with wood durability and deer browse resistance. We used the genomic realized relationship matrix for paternity assignment, maternal pedigree correction, and to estimate genetic parameters. We compared genomics-based (GBLUP) and two pedigree-based (ABLUP: polycross and reconstructed full-sib [FS] pedigrees) models. Models were extended to estimate dominance genetic effects. Pedigree reconstruction revealed significant unequal male contribution and separated the 26 PX families into 438 FS families. Traditional maternal PX pedigree analysis resulted in up to 51% overestimation in genetic gain and 44% in diversity. Genomic analysis resulted in up to 22% improvement in offspring breeding value (BV) theoretical accuracy, 35% increase in expected genetic gain for forward selection, and doubled selection intensity for backward selection. Overall, all traits showed low to moderate heritability (0.09-0.28), moderate genotype by environment interaction (type-B genetic correlation: 0.51-0.80), low to high expected genetic gain (6.01%-55%), and no significant negative genetic correlation reflecting no large trade-offs for multi-trait selection. Only three traits showed a significant dominance effect. GBLUP resulted in smaller but more accurate heritability estimates for five traits, but larger estimates for the wood traits. Comparison between all, genic-coding, genic-non-coding and intergenic SNPs showed little difference in genetic estimates. In summary, we show that GBLUP overcomes the PX limitations, successfully captures expected historical and hidden relatedness as well as linkage disequilibrium (LD), and results in increased breeding efficiency in WRC.

Reproductive ecology of male and female Strobili and mating system in two different populations of Pinus roxburghii

We studied several flowering traits, namely, male-female cone phenology, male-female cone production per tree, mating system, sex ratio, air-borne pollen grains and pollen migration, over four successive years in two different natural populations of P. roxburghii from Garhwal Himalaya, India. Assessment of each trait mentioned except pollen dispersion was done by selecting five representative trees randomly in each population. The pollen migration was studied on naturally isolated source trees. The pollen trapping was done in all directions up to 2.5 km. The average reproductive period in P. roxburghii was 36 days with 3–5 days protandry. There were significant year and population effects for male and female cone output and pollen grains production per tree. In mass production year (1999), an average production of pollen cone per tree was estimated as 42.44 ± 8.32 × 10³ at lower altitude and 28.1 ± 0.89 × 10³ at higher altitude. The controlled pollination results in high level of outcrossing with 90% seed setting. We conclude that the high male-female ratio and tremendous pollen production capacity in P. roxburghii indicate high male competition among trees within populations. The isolation strip of 600 m is considered minimal for the management of seed orchard.

Analysis of inbreeding depression in mixed-mating plants provides evidence for selective interference and stable mixed mating

Hermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates of selfing, driven by rapid purging of genetic load and loss of inbreeding depression (ID), but the substantial number of mixed-mating species observed in nature calls this prediction into question. Lower average ID reported for selfing than for outcrossing populations is consistent with purging and suggests that mixed-mating taxa in evolutionary transition will have intermediate ID. We compared the magnitude of ID from published estimates for highly selfing (r > 0.8), mixed-mating (0.2 ≤ r ≥ 0.8), and highly outcrossing (r < 0.2) plant populations across 58 species. We found that mixed-mating and outcrossing taxa have equally high average lifetime ID (δ= 0.58 and 0.54, respectively) and similar ID at each of four life-cycle stages. These results are not consistent with evolution toward selfing in most mixed-mating taxa. We suggest that prevention of purging by selective interference could explain stable mixed mating in many natural populations. We identify critical gaps in the empirical data on ID and outline key approaches to filling them.

Variation of selfing rate and inbreeding depression among individuals and across generations within an admixed Cedrus population

We investigated the variation and short-term evolution of the selfing rate and inbreeding depression (ID) across three generations within a cedar forest that was established from admixture ca 1860. The mean selfing rate was 9.5%, ranging from 0 to 48% among 20 seed trees (estimated from paternally inherited chloroplast DNA). We computed the probability of selfing for each seed and we investigated ID by comparing selfed and outcrossed seeds within progenies, thus avoiding maternal effects. In all progenies, the germination rate was high (88-100%) and seedling mortality was low (0-12%). The germination dynamics differed significantly between selfed and outcrossed seeds within progenies in the founder gene pool but not in the following generations. This transient effect of selfing could be attributed to epistatic interactions in the original admixture. Regarding the seedling growth traits, the ID was low but significant: 8 and 6% for height and diameter growth, respectively. These rates did not vary among generations, suggesting minor gene effects. At this early stage, outcrossed seedlings outcompeted their selfed relatives, but not necessarily other selfed seedlings from other progenies. Thus, purging these slightly deleterious genes may only occur through within-family selection. Processes that maintain a high level of genetic diversity for fitness-related traits among progenies also reduce the efficiency of purging this part of the genetic load.

Impacts of forest fragmentation on the mating system and genetic diversity of white spruce (Picea glauca) at the landscape level

We studied the mating system of white spruce (Picea glauca) in a landscape fragmented by agriculture in northern Ontario, Canada. We sampled 23 stands that ranged in size from 1 to >500 trees isolated by 250-3000 m from the nearest other stand. Six polymorphic allozyme loci from four enzyme systems were used to genotype approximately 10 000 embryos from 104 families. We detected no allele frequency heterogeneity in the pollen pool among stands or families (Phi(FT)=-0.025). Overall, estimates of outcrossing were high (t(m)=94% and mean t(s)=91%) but significantly different from unity. Bi-parental inbreeding (t(m)-t(s)=3.2%) was low but significantly different from zero. Allozyme-based outcrossing estimates did not differ significantly among three stand-size classes (SSCs): small (<10 trees), medium (10-100 trees) and large (> or =100 trees). The number of effective pollen donors was high in all SSCs, but was significantly lower in small stands (N(ep)=62.5) than in medium-sized and large stands (both N(ep)=143). The primary selfing rate was significantly higher in medium stands than in large stands. We found no significant difference in genetic diversity measures in the filial (seed) population among SSCs. Overall, these results indicate that white spruce stands in this fragmented landscape are resistant to genetic diversity losses, primarily through high pollen-mediated gene-flow and early selection against inbred embryos. We discuss the importance of using seed data, in conjunction with genetic data, to evaluate the impacts of fragmentation on natural populations.

Mating patterns, pollen dispersal, and the ecological maternal neighbourhood in a Prunus mahaleb L. population

Gender polymorphism, plant-animal interactions, and environmental heterogeneity are the three important sources of variation in mating system and pollen dispersal patterns. We used progeny arrays and paternity analysis to assess the effects of gender type and density level on variation in mating patterns within a highly isolated population of Prunus mahaleb, a gynodioecious species. All the adult trees in the population were sampled and located. The direct estimate of long-distance insect-mediated pollination events was low (< 10%). Gender expression deeply influenced the mating system, decreasing the outcrossing rates (t(m)) and the pollen pool diversity in hermaphrodite trees. Long intermate distances (> 250 m) were significantly more frequent among female mother trees. Variation in local tree density also affected pollen pool diversity and intermate distance, with a higher effective number of fathers (k(e)) and longer intermate distances for female trees in low-density patches. A canonical correlation analysis showed significant correlations between mating variables and the maternal ecological neighbourhood. Only the first canonical variable was significant and explained 78% of variation. Outcrossing rates tended to decrease, and the relatedness among the fathers tended to increase, when mother trees grew in dense patches with high cover of other woody species and taller vegetation away from the pine forest edge. We highlight the relevance of considering maternal ecological neighbourhood effects on mating system and gene flow studies as maternal trees act simultaneously as receptors of pollen and as sources of the seeds to be dispersed.

Post-pollination mechanisms promoting outcrossing in a self-fertile conifer,Thuja plicata(Cupressaceae)

In conifers, polyembryony (multiple embryos within an ovule) may decrease the number of seeds lost to random embryo abortion, and (or) increase the proportion of outcrossed seeds if outcrossed embryos out-compete selfed ones. Western redcedar (Thuja plicata Don ex D. Donn, Cupressaceae) is a conifer with a mixed (selfed and outcrossed) mating system and high self-fertility with simple (archegonial) polyembryony. To test whether polyembryony can decrease seed abortion or the proportion of selfed seedlings, we conducted controlled pollinations in a seed orchard in southwestern British Columbia. Four trees received a total of 48 pollination treatments consisting of self, outcross, or mixtures of self and outcross pollen. Enzyme electrophoresis identified selfed seeds in the mixed pollen treatments. Reduction in the proportion of filled seeds (seed set) owing to selfing was approximately 30% for three of the trees and 93% for the fourth. Following mixed pollinations we did not observe an increase in seed set attributable to polyembryony. However, when trees received high ratios of self-pollen they produced fewer selfed seedlings than expected, suggesting embryo competition. The consequences of these results on the mating system of western redcedar are discussed.Key words: conifer, Cupressaceae, embryonic lethals, inbreeding depression, polyembryony, Thuja plicata.