Genotypic variation of Cunninghamia lanceolata revealed by phenotypic traits and SRAP markers

Self Cite

Knowledge on population diversity and structure is of fundamental importance for conifer breeding programs. In this study, we concentrated on the development and application of high-density single nucleotide polymorphism (SNP) markers through a high-throughput sequencing technique termed as specific-locus amplified fragment sequencing (SLAF-seq) for the economically important conifer tree species, Chinese fir (Cunninghamia lanceolata). Based on the SLAF-seq, we successfully established a high-density SNP panel consisting of 108,753 genomic SNPs from Chinese fir. This SNP panel facilitated us in gaining insight into the genetic base of the Chinese fir advance breeding population with 221 genotypes for its genetic variation, relationship and diversity, and population structure status. Overall, the present population appears to have considerable genetic variability. Most (94.15%) of the variability was attributed to the genetic differentiation of genotypes, very limited (5.85%) variation occurred on the population (sub-origin set) level. Correspondingly, low F ST (0.0285-0.0990) values were seen for the sub-origin sets. When viewing the genetic structure of the population regardless of its sub-origin set feature, the present SNP data opened a new population picture where the advanced Chinese fir breeding population could be divided into four genetic sets, as evidenced by phylogenetic tree and population structure analysis results, albeit some difference in membership of the corresponding set (cluster vs. group). It also suggested that all the genetic sets were admixed clades revealing a complex relationship of the genotypes of this population. With a step wise pruning procedure, we captured a core collection (core 0.650) harboring 143 genotypes that maintains all the allele, diversity, and specific genetic structure of the whole population. This generalist core is valuable for the Chinese fir advanced breeding program and further genetic/genomic studies. breeder to address the population genetic architecture (genetic structure, diversity and relationship, etc.) and facilitate the accurate mating designs with parental analysis to accelerate the breeding progress [8]. The accessible molecular marker includes: (1) hybridization-based type such as restriction fragment length polymorphism (RFLP) and its modified forms, (2) PCR and electrophoresis-based type including random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), sequence-related amplified polymorphism (SRAP), inter simple sequence repeat (ISSR), and simple sequence repeat (SSR) etc., and (3) sequencing-based type dominated by single nucleotide polymorphism (SNP) [9][10][11]. Of these, SNPs have proved to be the most abundant form of variation within a species at genome level that provides more detailed insights into the genetic base of a population [10]. They have become more and more popular because they can be high-throughput detected through next-generation sequencing (NGS) at a moderate cost. Notably, the NGS-based SNP genoty...

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Chinese Fir Breeding in the High-Throughput Sequencing Era: Insights from SNPs

Zheng

Wei

et al. 2019

Self Cite

“…Each parent clone had at least four ramets of similar size and vigor at age 12. Three randomly selected ramets were measured for wood basic density (WBD) and hygroscopicity (Hy) with an increment core method described by Zheng et al [11]. In brief, a 5.02-mm increment core was taken at breast height (1.3 m) from each tree using a tree growth cone.…”

Section: Methodsmentioning

confidence: 99%

“…Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), an evergreen coniferous tree that occupies approximately 25% of plantations in southern China, has received a considerable breeding effort over the past 50 years, largely due to its great afforestation values and ecological contributions [10,11].…”

Section: Introductionmentioning

confidence: 99%

Assessing 62 Chinese Fir (Cunninghamia lanceolata) Breeding Parents in a 12-Year Grafted Clone Test

Zheng

Wang

et al. 2015

Self Cite

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is one of the major commercial conifer species in China. The present study concentrated on the assessment of growth, wood property traits, and strobili number in a 12-year grafted clone test of 62 Chinese fir breeding parents, aiming to describe the variation and correlations between these traits and to identify parent clones with the highest potential for future breeding. The results indicate that all of the growth (height, diameter at breast height, stem volume, crown-width) and wood property (wood basic density and hygroscopicity) traits varied significantly (p < 0.01) among clones, with coefficients of variation ranging from 7.6% to 30.6%. Furthermore, these traits consistently had a moderate to high (0.39-0.87) repeatability estimate (broad-sense heritability). Remarkable clonal differences were also observed for the production of male and female strobili. Phenotypic correlations among growth traits were strong (p < 0.01) and positive. Significantly negative correlations (p < 0.01 or 0.05) were found between wood basic density and growth (except for height) and hygroscopicity. The production of male and female strobili appeared to be significantly (p < 0.01) positively correlated with each other. A notable number of faster-growing parent clones were identified (n = 30); 11 of these had higher density wood with an average realized gain of 10.5% in diameter, and a 5.4% gain in wood basic density. When selection was made for growth and strobili, 10 faster-growing parent clones with medium to high production of female strobili were identified. OPEN ACCESSForests 2015, 6 3800

“…Chinese fir has received considerable breeding effort over the past 50 years [10]. The systematic breeding programs started in 1960s and remarkable successes were achieved [11].…”

Section: Introductionmentioning

confidence: 99%

Effects of Sucrose, Boric Acid, pH, and Incubation Time on in Vitro Germination of Pollen and Tube Growth of Chinese fir (Cunnighamial lanceolata L.)

Fragallah

Lin

et al. 2019

In vitro pollen germination provides a novel approach and strategy to accelerate genetic improvement of tree breeding. Studies about pollen germination and tube growth of Chinese fir are limited. Therefore, this study aimed to investigate the effects of sucrose, boric acid, pH, and time of incubation on pollen germination and tube growth. Pollen from 9 clones were selected. In vitro germination was performed in basic media as control, and in different concentrations of sucrose (0, 10 and 15%), boric acid (0.01, 0.1 and 0.2%), and pH levels (4.5, 5 and 7). Pollen germination rates and tube growth were recorded periodically at 1, 12, 24, and 48 h. The results showed that sucrose imposes significant effects on pollen germination and tube growth. The effects are most obvious at concentration of 15%. Boric acid significantly promoted germination and tube growth. The promotion was most notable in lower concentration of 0.01%. The media adjusted to pH 7.0 boosted the germination and pollen tube growth. The optimum time of incubation was 24 and 48 h for pollen germination and tube growth, respectively. Sucrose, pH, and time of incubation were positively correlated, whereas boric acid negatively correlated with pollen germination and tube growth. This study provided experimental evidences for selecting viable pollens for Chinese fir breeding.