Dataset Information

Genetic diversity and structure of the 4^th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook).

ABSTRACT: Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4^th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4^th cycle breeding population was high with nucleotide diversity (P_i ) of 0.003, and H_o and H_e of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (F_st < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.

SUBMITTER: Jing Y

PROVIDER: S-EPMC9911867 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Genetic diversity and structure of the 4th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook).

Jing Yonglian Y Bian Liming L Zhang Xuefeng X Zhao Benwen B Zheng Renhua R Su Shunde S Ye Daiquan D Zheng Xueyan X El-Kassaby Yousry A YA Shi Jisen J

Frontiers in plant science 20230127

Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of th ...[more]

PMID: 36778690

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Project description:BackgroundThe molecular mechanisms that govern cambial activity in angiosperms are well established, but little is known about these molecular mechanisms in gymnosperms. Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), a diploid (2n = 2x = 22) gymnosperm, is one of the most important industrial and commercial timber species in China. Here, we performed transcriptome sequencing to identify the repertoire of genes expressed in cambium tissue of Chinese fir.Methodology/principal findingsBased on previous studies, the four stage-specific cambial tissues of Chinese fir were defined using transmission electron microscopy (TEM). In total, 20 million sequencing reads (3.6 Gb) were obtained using Illumina sequencing from Chinese fir cambium tissue collected at active growth stage, with a mean length of 131 bp and a N50 of 90 bp. SOAPdenovo software was used to assemble 62,895 unigenes. These unigenes were further functionally annotated by comparing their sequences to public protein databases. Expression analysis revealed that the altered expression of six homologous genes (ClWOX1, ClWOX4, ClCLV1-like, ClCLV-like, ClCLE12, and ClPIN1-like) correlated positively with changes in cambial activities; moreover, these six genes might be directly involved in cambial function in Chinese fir. Further, the full-length cDNAs and DNAs for ClWOX1 and ClWOX4 were cloned and analyzed.ConclusionsIn this study, a large number of tissue/stage-specific unigene sequences were generated from the active growth stage of Chinese fir cambium. Transcriptome sequencing of Chinese fir not only provides extensive genetic resources for understanding the molecular mechanisms underlying cambial activities in Chinese fir, but also is expected to be an important foundation for future genetic studies of Chinese fir. This study indicates that ClWOX1 and ClWOX4 could be possible reverse genetic target genes for revealing the molecular mechanisms of cambial activities in Chinese fir.

Project description:: Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is one of the most important coniferous evergreen tree species in South China due to its desirable attributes of fast growth and production of strong and hardy wood. However, the yield of Chinese fir is often inhibited by aluminum (Al) toxicity in acidic soils of South China. Understanding the molecular mechanisms of Chinese fir root responses to Al toxicity might help to further increase its productivity. Here we used the Illumina Hiseq4000 platform to carry out transcriptome analysis of Chinese fir roots subjected to Al toxicity conditions. A total of 88.88 Gb of clean data was generated from 12 samples and assembled into 105,732 distinct unigenes. The average length and N50 length of these unigenes were 839 bp and 1411 bp, respectively. Among them, 58362 unigenes were annotated through searches of five public databases (Nr: NCBI non-redundant protein sequences, Swiss-Prot: A manually annotated and reviewed protein sequence database, GO: Gene Ontology, KOG/COG: Clusters of Orthologous Groups of proteins, and KEGG: the Kyoto Encyclopedia of Genes and Genomes database), which led to association of unigenes with 44 GO terms. Plus, 1615 transcription factors (TFs) were functionally classified. Then, differentially expressed genes (DEGs, |log2(fold change)| ≥ 1 and FDR ≤ 0.05) were identified in comparisons labelled TC1 (CK-72 h/CK-1 h) and TC2 (Al-72 h/Al-1 h). A large number of TC2 DEGs group were identified, with most being down-regulated under Al stress, while TC1 DEGs were primarily up-regulated. Combining GO, KEGG, and MapMan pathway analysis indicated that many DEGs are involved in primary metabolism, including cell wall metabolism and lipid metabolism, while other DEGs are associated with signaling pathways and secondary metabolism, including flavonoids and phenylpropanoids metabolism. Furthermore, TFs identified in TC1 and TC2 DEGs represented 21 and 40 transcription factor families, respectively. Among them, expression of bHLH, C2H2, ERF, bZIP, GRAS, and MYB TFs changed considerably under Al stress, which suggests that these TFs might play crucial roles in Chinese fir root responses to Al toxicity. These differentially expressed TFs might act in concert with flavonoid and phenylpropanoid pathway genes in fulfilling of key roles in Chinese fir roots responding to Al toxicity.

Dataset Information

Genetic diversity and structure of the 4^th cycle breeding population of Chinese fir (Cunninghamia lanceolata (lamb.) hook).

Publications

Genetic diversity and structure of the 4<sup>th</sup> cycle breeding population of Chinese fir (<i>Cunninghamia lanceolata</i> (lamb.) hook).

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