Balancing seed yield and breeding value in clonal seed orchards

Seed orchards should produce seeds that are both abundant and of high genetic value. This study suggests methods to achieve such a compromise and study their efficiency. The methods were applied on data obtained from 41 seed orchard clones of Scots pine from mid-Sweden. The value of the seed orchard crop was set as a function of its breeding value, the amount of seeds produced and their gene diversity, measured as the effective number of clones. The proportion of ramets of different clones that maximized this value was regarded as the optimum for deployment of the clones in a seed orchard. The results were compared with truncation selection for breeding value, truncation selection for clone benefit (the product of seed production and breeding value) and linear deployment (where ramets are deployed linearly in relation to breeding value). The influence of two parameters was studied: the relative importance of breeding value for seed value and the size of the penalty for reducing the value of the seed crop with respect to lost gene diversity. The conventional wisdom is to select the clones with the highest breeding values, but that turned out to be the most inferior alternative studied. Clone benefit truncation provided a good approximation to optimal benefit for cases, where the effective number was low and dependence of breeding value limited.     

Genetic thinning of clonal seed orchards using linear deployment may improve both gain and diversity

The linear deployment algorithm defines a straight line relationship between the number of ramets and the breeding value of a given clone. However, when used to determine thinning in clonal seed orchards, there is an upper limit, determined by the number of ramets in the seed orchard prior to thinning. Linear deployment thinning maximises genetic gain and effective clone number whilst minimising thinning intensity, thus both production and genetic diversity are optimised. Here two applications of linear deployment to Swedish Norway spruce seed orchards are described.     

Impact of Fertility Variation on Gene Diversity and Drift in two Clonal Seed Orchards of Teak (Tectona grandis Linn. f.)

Two 25 year old teak clonal seed orchards comprising 15 (CSO-I) and 20 clones (CSO-II), respectively, selected mostly from moist forests of Western Ghats (latitude 10° N) in southern India, were evaluated for fertility, offspring diversity, and genetic drift. The orchards differed in fertility of clones as well as flower and fruit production per ramet. Fertility was highly skewed in CSO-II, where one clone (originating from higher latitude −17° N, in Eastern Ghats of peninsular India) produced 55% of the fruits and 68% of the flowers in the orchard, in contrast to a similar contribution from four most fertile clones in CSO-I. Fertility variation, measured as `sibling coefficient' (1.7 in CSO-I and 8.3 in CSO-II), was high in CSO-II resulting in high coancestry and low effective population size (3 times lower than CSO-I) in the seed crop. In CSO-I, 58% of the clones contributed effectively to seed production compared to only 12% effective contribution resulting in eight times higher genetic drift in CSO-II. Placing limits on how much seed can be collected per clone might be useful in restricting over representation of highly reproductive clones thereby increasing genetic diversity in the seed crop.     

Female fertility variation in mature Pinus sylvestris clonal seed orchards

Abstract

Female fertility is the basis for the output of seeds from clonal orchards and its variation is of major interest for the economics and biology of seed orchards, especially for the efficiency and diversity of seed orchard crops. Assessments of female fertility variation in 10 mature (>15 years old) seed orchards of Scots pine (Pinus sylvestris L.) were evaluated and compared. Depending on the individual orchard, fertility variation for each clone was assessed in slightly different ways, e.g. number of strobili, cones, seeds or litre of cones per ramet. Assessments in five of the orchards were made over consecutive years. The main result was that the clonal variation in mean female fertility per surviving ramet was lower than expected from the literature; the Kang–Lindgren sibling coefficient (Ψ) within individual years averaged 1.35. The variation between ramets within clones and years was of similar magnitude as that between clones. Clone by year interactions were noticeable, but were slightly lower than the variation between as well as that within clones in individual years. There was considerable variation in the variance components between years. The limited variation in female fertility indicated that it should not be a selection criterion when selecting clones for a seed orchard. Furthermore, it will not result in large differences between clones in seed set or large reductions in gene diversity in productive Scots pine seed orchards.     

马尾松种子园优良无性系的选择与评价

通过对马尾松种子园132个无性系种子产量性状调查与木材比重测定及种子园自由授粉子代8年生生长性状调查,在统计分析、相关分析基础上采用综合评分法进行优良无性系的选择,入选率为20%。结果表明:对马尾松种子园无性系再选择,以营建改良代种子园是可行的。8年生子代材积可获得改良增益10.6%,木材比重可获得4.6%的增益,种子园单株产种量可获得增益37.5%,选择效果明显,达到提高种子园产量、增加改良增益的目的。     

Advanced-generation wind-pollinated seed orchard design

Design criteria for advanced-generation seed orchards are discussed with particular emphasis on the comparison between systematic and randomized designs. A simulation approach was used to compare expected genetic gain from a variety of systematic designs with varying numbers of clones and effective population sizes for intermediate (N=201) and large (N=2001) breeding programs. The types of designs examined included orchards containing 1) only parental or backward selections, 2) offspring or forward selections, and 3) a combination of parental and offspring selections. Assuming random mating, parental orchards always offer more genetic gain than offspring orchards; this difference increases as selection intensity increases. Including the best clones in higher frequencies can yield approximately a 1% marginal increase in genetic gain compared to equal representation for all clones.     

Juvenile radiata pine clonal seed orchard management in Galicia (NW Spain)

A juvenile radiata pine clonal seed orchard (Pinus radiata D. Don) in Sergude (northwestern Spain), comprising 57 clones, was evaluated for fertility, offspring diversity and genetic drift during 4 years. Flower and fruit production was used to asses clone fertility in the orchard. Fertility variation measured as “sibling coefficient” was found to be an average of 1.5, having high genetic diversity (0.99) and low coancestry (0.013). The clones varied in fertility from year to year. Effective population size in the orchard was between 35 and 40, indicating that between 60.30 and 69 %, the clones contributed effectively to seed yield. One way to improve seed yield in the orchard is by increasing the effective population size. Thinning and pruning highly reproductive clones of gibberellin application might be useful in increasing effective population size. The orchard’s parental balance showed consistent improvement over time. Cone and seed characteristics were also investigated. The results showed that significant genetic variation exists among clones for cone width and length; total, sound and empty seed number; as well as 100 seed weight. The seed orchard is still in a juvenile phase; moreover, the broad-sense heritability and variation data obtained in this study could be very valuable in the management practices of the existing radiata pine clonal seed orchard and can be also used for better planning of advanced generation of clonal seed orchards in Spain.     

Magnitude and efficiency of genetic diversity captured from seed stands of <Emphasis Type="Italic">Pinus nigra</Emphasis> (Arnold) subsp. <Emphasis Type="Italic">pallasiana</Emphasis> in established seed orchards and plantations

To test how efficiently plantations and seed orchards captured genetic diversity from natural Anatolian black pine (Pinus nigra Arnold subspecies pallasiana Holmboe) seed stands, seed sources were chosen from 3 different categories (seed stands (SS), seed orchards (SO) and plantations (P)) comprising 4 different breeding zones of the species in Turkey. Twenty-five trees (mother trees) were selected from each SS, SO and P seed sources and were screened with 11 Random Amplified Polymorphic DNA (RAPD) markers. Estimated genetic diversity parameters were found to be generally high in all Anatolian black pine seed sources and the majority of genetic diversity is contained within seed sources (94%). No significant difference in genetic diversity parameters (numbers of effective alleles, % of polymorphic loci and heterozygosity) among seed source categories was found, except for a slight increase in observed heterozygosities in seed orchards. For all seed source categories, observed heterozygosity values were higher (H_o = 0.49 for SS, 0.55 for SO and 0.49 for P) than expected ones (H_e = 0.40 for SS, 0.39 for SO and 0.38 for P) indicating the excess of heterozygotes. In general, genetic diversity in seed stands has been transferred successfully into seed orchards and plantations. However, the use of seeds from seed orchards can increase the amount of genetic diversity in plantations further. The study also demonstrated that number of plus-tree clones (25–38) used in the establishment of seed orchards was adequate to capture the high level of diversity from natural stands.     

Parental participation in progeny and effective population sizes in experimental seed orchards of wild cherry Prunus avium L. (Batsch)

Parents and progenies genetic diversity, and male and female contributions to the seed crop were assessed in three experimental Prunus avium seed orchards. Collected data were used to compare different effective population sizes, based on phenological, seed crop and paternity analysis. Our results did not show any difference of genetic diversity between parents and progenies. A limited pollen pollution was detected. We showed that distance and coflowering among clones had a significant effect on effective pollination, and a significant effect of the production of flowers was revealed in one of the seed orchards. Our study also revealed a quite low number of effective size of fathers per mother, but high effective sizes of mothers, fathers and parents at the level of the seed orchard. Finally, the calculation of effective size of mothers, fathers and parents was not highly modified when having the complete information based on the paternity analysis.     

Breeding without breeding: selection using the genomic best linear unbiased predictor method (GBLUP)

We demonstrate, using height data from a clonal trial, how the genomic best linear unbiased predictor method (GBLUP) is ideal for determining future breeding potential in situations (either in plantations or wild stands) where high mortality due to biotic or abiotic factors has occurred. The method is effective because it does not require the development of structured pedigree or classical progeny testing, rather it uses DNA fingerprinting to determine the genealogical relationship among individuals. The resulting genetic network is known as the realized relationship matrix, which in turn is used in classical quantitative genetics analyses to determine the genetic worth of all fingerprinted individuals. Selection of desirable individuals among the surviving population is aimed at maximizing genetic diversity even when the original genetic source is unknown. This is accomplished by determining the number of founder genome equivalents which can be used to estimate the inbreeding effective population size. During the selection phase, genetic diversity can be balanced against genetic gain so that diversity is maximized while gain for any particular attribute is optimized.     

Genetic variation, mating patterns and gene flow in a Pinus pinaster Aiton clonal seed orchard

? Relatedness among parents, variation in clonal fertility and background pollination deviate the realized genetic gain and the gene diversity of open pollinated seed orchard from expectation, in particular in wind pollinated species such as Pinus pinaster Aiton.

? This work investigates the genetic variation, the mating system and the pollen contamination in a P. pinaster clonal seed orchard (CSO), by screening the 60 clones from the CSO and the seeds collected from 21 mother-trees with three nuclear microsatellites.

? The expected diversity was similar, but the observed heterozygosity decreased 20% in the progenies compared with the parental trees. The outcrossing rate was 90.1%, the biparental inbreeding 21.7% computed through a multilocus approach, and the observed selfing 3.9%. The observed gene flow from outside the CSO was 52.4%.

? From the results we concluded that the observed gene flow and the biparental inbreeding were high, and care should be taken in the implementation and management of future CSO, in particular clones should be checked for relatedness and the ramet number could be directly proportional to their breeding value.

     

Variation in effective number of clones in seed orchards

The effective number of clones (N _c) wasestimated for 255 conifer clonal seed orchards in Finland, Korea, andSweden, based on the variation in the number of ramets among clones. Themean census number of clones (N) varied from 70, in 13 KoreanPinus koraiensis seed orchards, to 139 in 176 Finnish Pinussylvestris seed orchards. The mean effective number of clones(N _c) was 66, with a range from 10 to 421. One fifthof the orchards had N _c between 10 and 40, and twothirds between 41 and 160. On average, the relative effective number ofclones (N _r =N _c/N) was 0.74, with a range from 0.2to almost 1.0. Thus, the census number of clones in a seed orchard isgenerally rather informative, but the effective number of clones is moreinformative. Many of these first-generation seed orchards wereestablished with an intention to have near-equal numbers of ramets foreach clone. The use of effective number of clones may be more importantin future seed orchards and genetically thinned seed orchards.     

马尾松二代无性系种子园遗传多样性和交配系统分析

运用12对SSR引物,对马尾松二代无性系种子园内61个亲本及其中8个无性系单株的320个子代进行研究。结果显示:子代群体包含亲本群体的所有等位基因,子代与亲本具有同样高的遗传多样性,子代群体的F为0.045,纯合子过剩的现象不明显;树冠北面子代遗传多样性并未因其雌、雄球花量较树冠南面减少而有明显的降低;雌雄均衡和偏雌型植株子代遗传多样性基本一致,以偏雌型植株子代略大,二者F趋于0,子代基本符合哈温平衡。种子园异交率较高,多位点异交率为1.098,子代亲本的近交现象不显著(tm-ts=-0.033);树冠南面多位点与单位点异交率均高于树冠北面;偏雌与雌雄均衡型植株的多位点异交率基本相当,雌雄均衡型植株并未因其雌、雄球花量比例较偏雌型植株减小而呈现异交率明显降低的现象,2种类型植株的近交指数均接近于0。整体而言,马尾松二代种子园子代仍具有丰富的遗传多样性,无性系间基因交流相对充分,子代亲本近交现象不明显。     

Clonal variations in nutritional components of <Emphasis Type="Italic">Pinus koreansis</Emphasis> seeds collected from seed orchards in Northeastern China

From four Korean pine (Pinus koraiensis) orchards, 60 clones were selected and analyzed for the fatty acid and amino acid components of the seeds to reveal the variations and correlations of the seed characteristics among the clonal source orchards and clones. The nutritional components of the seeds of the P. koraiensis trees exhibited rich genetic variation; the variation coefficient of the fatty acids was 2.24–66.83 %, while the variation coefficient of the amino acids was 14.70–38.88 %. Relatively high genetic-improvement potential exists for the nutritional components of the seeds. The phenotypic differentiation of the fatty acid and amino acid components reveals that variation within the population (85.18 %) was the primary source for the variation of the fatty acid components; variation among the orchards (63.08 %) was the primary source of the variation of the amino acid components. Data drawn from various clonal source orchards all showed that the seed characteristics were highly controlled by heritability (h² > 80 %), and the seed characteristics of the P. koraiensis trees exhibited a similar genetic gain trend. The principal components were analyzed to obtain the comprehensive principal component value for each clonal seed orchard. Twelve clones were selected based on a clonal selection rate of 20 %. Correlation and multiple stepwise-regression analyses were conducted, considering different location conditions, to reveal the stable correlations between the seed characteristics to facilitate improvements of the seed yield of P. koraiensis trees and the clonal selection. Species of real characteristics in P. koraiensis were controlled by higher heritability. Genetic gain was obtained by selecting of superior clones.     

Genetic Diversity and Mating System Analysis of Pinus massoniana in Second-Generation Clonal Seed Orchard

A total 61 clone parents and 320 open-pollination progenies from 8 clone individuals were identified by 12 polymorphic SSR loci.The result showed that the level of genetic diversity in progeny population was the same as in maternal population, progeny population had all alleles detected in maternal population,and there were not obvious surplus phenomenon of homozygotes in progeny population (F= 0.046).The south crown had more strobili than the north crown,however the genetic diversity of the north crown strobili was not substantially reduced.The progeny of neutral trees had the same level of genetic diversity as in the progeny of partial female trees,with the fixation index tended to be zero,which was accorded with Hardy-Weinberg equilibrium.The multilocus outcrossing rate in the seed orchard was 1.097,and there was no significant inbreeding between parents(t_m-t_s= - 0.031).The multilocus outcrossing rate and singlelocus outcrossing rate in the south crown were higher than that in the north crown.The multilocus outcrossing rate of partial female trees was the same as in neutral trees,and the neutral tree had no obvious declining outcrossing rate with reduced proportion of female and male strobilus compared with partial female tree, with the fixation index tended to be zero.The progeny of the second generation clonal seed orchard still had rich genetic diversity,gene exchange among clones was relatively sufficient,and biparental inbreeding was not significant.     

杉木无性系年龄段球果分布研究

根据广东小坑、安徽西田2个杉木种子园26个无性系，每系3个标准株，计78个分株各年龄段的球果分布资料，研究分析了杉木无性系水平的年龄段球果分布状况，进一步认识了杉木无性系球果的着生规律，为高世代杉木种子园的无性系再选择，进行了有益的探讨。     

Variation in cone and seed characters in clonal seed orchards of <Emphasis Type="Italic">Pinus sylvestris</Emphasis>

Cone and seed characters were observed on top, middle and bottom portions of tree crown in 3 ramets/clone in three Turkish Pinus sylvestris seed orchards. Broad sense heritability (clonal repeatability), and correlations among characters were estimated. Around one quarter of the seed production occurred in the top portion, half in the middle and one quarter in the bottom portion of the crown for all orchards. The percentage of filled seeds varied little with the crown position, indicating more or less similar levels of selfing in the bottom of the crown as in the top. The seed weight was typically 11 mg. Differences were found for studied cone and seed characters among orchards and crown positions. Variation among grafts within clone was higher than among clones for most characters. The heritability was on average below 0.5 (e.g., cone diameter, number of filled seed per cone) and rarely rose above that (e.g., cone form, length/diameter; percentage of filled seed) for any individual characters. The coefficient of variation within clones was often higher than among clones. Thus, non-genetic factors seem often more important for the variation in performance of grafts than their genetic constitution. Cone form (length/diameter) was the character where the clone influence was the strongest. Cone number and cone dry weight showed significant correlations with seed characters (numbers of total and filled seed, percentage and weight of filled seeds). Significant correlation was found between seed characters.     

Variability in seed traits and genetic divergence in a clonal seed orchard of Dalbergia sissoo Roxb.

The variations in seed and pod traits, genetic superiority and genetic divergence were evaluated for a Clonal Seed Orchard (CSO) of Dalbergia sissoo Roxb. at Bithmera, India consisting of 20 clones from different agro-climatic conditions of four northern states (Uttar Pradesh, Uttarakhand, Haryana and Rajasthan). The seeds and pods of various clones in the orchard exhibited significant variability in size, weight and other characters. Significant positive correlations were observed between seed length and seed width (p<0.05), seed length and seed thickness (p<0.01), seed length and seed weight (p<0.01), seed thickness and seed weight (p<0.01), seed length and germination value (p<0.05). The genetic parameters for seed and pod traits also showed a wide range of variations in the orchard. Heritability values were found to be over 50 percent for most of the seed and pod traits. Seed weight, seed length and seed thickness showed high heritability values coupled with maximum genetic gain for these characters. Ward’s minimum variance dendrogram of clones of D. sissoo showed three distinct clusters; cluster 1 was the largest with 12 better clones whereas cluster 2 and 3 consisting of seven moderate clones and one poor clone, respectively. Mean cluster values showed sufficient variation among the clusters for seed weight, germination value and seed length. The possible hybridization between best clones of cluster 1 to the disease resistant clone of cluster 2 (resistant against deadly Gandoderma lucidum root rot disease of D. sissoo) is also suggested for further breeding programmes of the species. The deployment of clone 194 (better performed and disease resistant) is also recommended in future plantation programmes of D. sissoo in northern India.     

Optimization of genetic gain and diversity in seed orchard crops considering variation in seed germination

Abstract

Balancing genetic gain and diversity in seed orchard crops is of a major regeneration importance. Here we extend our earlier work on the development of an optimization protocol that maximizes crops' genetic gain at any predefined diversity level, considering parental reproductive output, co-ancestry, and inbreeding, by incorporating variation in seed germination as an input. Variation in seed germination capacity substantially affected seedlots' genetic diversity by either under- or overestimating their effective population size; however, genetic gains were robust and their differences were negligible. The contrasting results of gain and diversity support the inclusion of the germination capacity, when available, in the optimization protocol.     

Mating patterns,genetic composition and diversity levels in two seed orchards with few clones—Impact on planting crop

Paternity analyses using microsatellites were conducted in two conifer clonal seed orchards (CSOs). The aim was to study mating patterns and potential dysfunctions such as unbalanced male contribution, and how these factors influence genetic diversity. The effect of unequal male contribution was quantified by the status number (N_S), which reflects build up of coancestry in the seed orchard crop due to low number of clones and unequal male contribution. This approach was also used to quantify the effect of clonal differences in germination percentages on effective population sizes. Furthermore the genetic diversity of the Abies alba and Larix kaempferi CSOs was compared to other alternative seed sources via observed heterozygosity and allelic richness.