Construction of a High-Density Genetic Map and Identification of Leaf Trait-Related QTLs in Chinese Bayberry (Myrica rubra)

Chinese bayberry (Myrica rubra) is an economically important fruit tree that is grown in southern China. Owing to its over 10-year seedling period, the crossbreeding of bayberry is challenging. The characteristics of plant leaves are among the primary factors that control plant architecture and potential yields, making the analysis of leaf trait-related genetic factors crucial to the hybrid breeding of any plant. In the present study, molecular markers associated with leaf traits were identified via a whole-genome re-sequencing approach, and a genetic map was thereby constructed. In total, this effort yielded 902.11 Gb of raw data that led to the identification of 2,242,353 single nucleotide polymorphisms (SNPs) in 140 F1 individuals and parents (Myrica rubra cv. Biqizhong × Myrica rubra cv. 2012LXRM). The final genetic map ultimately incorporated 31,431 SNPs in eight linkage groups, spanning 1,351.85 cM. This map was then used to assemble and update previous scaffold genomic data at the chromosomal level. The genome size of M. rubra was thereby established to be 275.37 Mb, with 94.98% of sequences being assembled into eight pseudo-chromosomes. Additionally, 18 quantitative trait loci (QTLs) associated with nine leaf and growth-related traits were identified. Two QTL clusters were detected (the LG3 and LG5 clusters). Functional annotations further suggested two chlorophyll content-related candidate genes being identified in the LG5 cluster. Overall, this is the first study on the QTL mapping and identification of loci responsible for the regulation of leaf traits in M. rubra, offering an invaluable scientific for future marker-assisted selection breeding and candidate gene analyses.

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Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

BMC Plant Biology ◽

10.1186/s12870-019-2207-y ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Nan Lu ◽

Miaomiao Zhang ◽

Yao Xiao ◽

Donghua Han ◽

Ying Liu ◽

...

Keyword(s):

Plant Growth ◽

Genetic Map ◽

Average Distance ◽

Leaf Traits ◽

Interval Mapping ◽

High Density ◽

Nucleotide Polymorphisms ◽

Significant Qtls ◽

Leaf Trait ◽

Catalpa Bungei

Abstract Background Catalpa bungei is an important tree species used for timber in China and widely cultivated for economic and ornamental purposes. A high-density linkage map of C. bungei would be an efficient tool not only for identifying key quantitative trait loci (QTLs) that affect important traits, such as plant growth and leaf traits, but also for other genetic studies. Results Restriction site-associated DNA sequencing (RAD-seq) was used to identify molecular markers and construct a genetic map. Approximately 280.77 Gb of clean data were obtained after sequencing, and in total, 25,614,295 single nucleotide polymorphisms (SNPs) and 2,871,647 insertions-deletions (InDels) were initially identified in the genomes of 200 individuals of a C. bungei (7080) × Catalpa duclouxii (16-PJ-3) F1 population and their parents. Finally, 9072 SNP and 521 InDel markers that satisfied the requirements for constructing a genetic map were obtained. The integrated genetic map contained 9593 pleomorphic markers in 20 linkage groups and spanned 3151.63 cM, with an average distance between adjacent markers of 0.32 cM. Twenty QTLs for seven leaf traits and 13 QTLs for plant height at five successive time points were identified using our genetic map by inclusive composite interval mapping (ICIM). Q16–60 was identified as a QTL for five leaf traits, and three significant QTLs (Q9–1, Q18–66 and Q18–73) associated with plant growth were detected at least twice. Genome annotation suggested that a cyclin gene participates in leaf trait development, while the growth of C. bungei may be influenced by CDC48C and genes associated with phytohormone synthesis. Conclusions This is the first genetic map constructed in C. bungei and will be a useful tool for further genetic study, molecular marker-assisted breeding and genome assembly.

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Genetic Diversity of Chinese Bayberry (Myrica rubra Sieb. et Zucc.) Accessions Revealed by Amplified Fragment Length Polymorphism

HortScience ◽

10.21273/hortsci.44.2.487 ◽

2009 ◽

Vol 44 (2) ◽

pp. 487-491 ◽

Cited By ~ 13

Author(s):

Shuiming Zhang ◽

Zhongshan Gao ◽

Changjie Xu ◽

Kunsong Chen ◽

Guoyun Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Length Polymorphism ◽

Fragment Length ◽

Fragment Length Polymorphism ◽

Southern China ◽

Genetic Relationships ◽

Amplified Fragment Length Polymorphism ◽

Group Method ◽

Chinese Bayberry ◽

Myrica Rubra

Amplified fragment length polymorphism (AFLP) was used to analyze genetic diversity of 100 accessions of Chinese bayberry (Myrica rubra Sieb. et Zucc.), one of the widely cultivated fruit tree crops in southern China. Six E-NN/M-NNN primer combinations were selected and a total of 236 bands were obtained, of which 177 were polymorphic (75.01%). An unweighted pair-group method of the arithmetic averages (UPGMA) was used to analyze the genetic relationships. The Dice's similarity coefficient among the Chinese bayberry accessions ranged from 0.75 to 1.00 and was 0.49 between Chinese bayberry and wax myrtle (M. cerifera L.). The 100 accessions of Chinese bayberry were clustered into two groups and seven subgroups. Subgrouping of Chinese bayberry was not related to the sex of the plant and color or size of the ripe fruit, but to some extent the region where the accession originated. However, the accessions from the same region did not necessarily belong to the same group or subgroup, which suggested the presence of extensive gene flow among different regions. Furthermore, close relationships between some morphologically similar accessions were found.

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Functional analysis of differentially expressed proteins in Chinese bayberry ( Myrica rubra Sieb. et Zucc.) fruits during ripening

Food Chemistry ◽

10.1016/j.foodchem.2015.06.023 ◽

2016 ◽

Vol 190 ◽

pp. 763-770 ◽

Cited By ~ 7

Author(s):

Yi-Yong Chen ◽

Ze-Huang Zhang ◽

Can-Yu Zhong ◽

Xiao-Min Song ◽

Qi-Hua Lin ◽

...

Keyword(s):

Functional Analysis ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Chinese Bayberry ◽

Myrica Rubra

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The role of MrbHLH1 and MrMYB1 in regulating anthocyanin biosynthetic genes in tobacco and Chinese bayberry (Myrica rubra) during anthocyanin biosynthesis

Plant Cell Tissue and Organ Culture (PCTOC) ◽

10.1007/s11240-013-0361-8 ◽

2013 ◽

Vol 115 (3) ◽

pp. 285-298 ◽

Cited By ~ 34

Author(s):

Xiao-Fen Liu ◽

Xue-Ren Yin ◽

Andrew C. Allan ◽

Kui Lin-Wang ◽

Yan-Na Shi ◽

...

Keyword(s):

Anthocyanin Biosynthesis ◽

Biosynthetic Genes ◽

Chinese Bayberry ◽

Myrica Rubra ◽

Anthocyanin Biosynthetic Genes

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Dietary compound proanthocyanidins from Chinese bayberry (Myrica rubra Sieb. et Zucc.) leaves inhibit angiogenesis and regulate cell cycle of cisplatin-resistant ovarian cancer cells via targeting Akt pathway

Journal of Functional Foods ◽

10.1016/j.jff.2017.11.045 ◽

2018 ◽

Vol 40 ◽

pp. 573-581 ◽

Cited By ~ 9

Author(s):

Yu Zhang ◽

Shiguo Chen ◽

Chaoyang Wei ◽

Gary O. Rankin ◽

Yon Rojanasakul ◽

...

Keyword(s):

Cell Cycle ◽

Ovarian Cancer ◽

Cancer Cells ◽

Akt Pathway ◽

Ovarian Cancer Cells ◽

Chinese Bayberry ◽

Myrica Rubra

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Dw2, a New Dwarfing Locus in Apple Rootstocks and Its Relationship to Induction of Early Bearing in Apple Scions

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.139.2.87 ◽

2014 ◽

Vol 139 (2) ◽

pp. 87-98 ◽

Cited By ~ 33

Author(s):

Gennaro Fazio ◽

Yizhen Wan ◽

Dariusz Kviklys ◽

Leticia Romero ◽

Richard Adams ◽

...

Keyword(s):

Genetic Map ◽

Production Systems ◽

Breeding Population ◽

Breeding Strategy ◽

Nucleotide Polymorphisms ◽

Apple Rootstock ◽

Apple Rootstocks ◽

Yield Data ◽

Trait Locus ◽

Rootstock Breeding

The ability of certain apple rootstocks to dwarf their scions has been known for centuries and their use revolutionized apple (Malus ×domestica) production systems. In this investigation, several apple rootstock breeding populations, planted in multiple replicated field and pot experiments, were used to ascertain the degree of dwarfing when grafted with multiple scions. A previous genetic map of a breeding population derived from parents ‘Ottawa 3’ (O.3) and ‘Robusta 5’ (R5) was used for quantitative trait locus (QTL) analysis of traits related to scion vigor suppression, induction of early bearing, and other tree size measurements on own-rooted and grafted trees. The analysis confirmed a previously reported QTL that imparts vigor control [Dw1, log of odds (LOD) = 7.2] on linkage group (LG) 5 and a new QTL named Dw2 (LOD = 6.4) on LG11 that has a similar effect on vigor. The data from this population were used to study the interaction of these two loci. To validate these findings, a new genetic map comprised of 1841 single-nucleotide polymorphisms was constructed from a cross of the dwarfing, precocious rootstocks ‘Geneva 935’ (G.935) and ‘Budagovsky 9’ (B.9), resulting in the confirmation and modeling of the effect of Dw1 and Dw2 on vigor control of apple scions. Flower density and fruit yield data allowed the identification of genetic factors Eb1 (LOD = 7.1) and Eb2 (LOD = 7.6) that cause early bearing of scions, roughly colocated with the dwarfing factors. The major QTL for mean number of fruit produced per tree colocated with Dw2 (LOD = 7.0) and a minor QTL was located on LG16 (LOD = 3.5). These findings will aid the development of a marker-assisted breeding strategy, and the discovery of additional sources for dwarfing and predictive modeling of new apple rootstocks in the Geneva® apple rootstock breeding program.

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Predicting Leaf Trait Variability as a Functional Descriptor of the Effect of Climate Change in Three Perennial Grasses

Diversity ◽

10.3390/d11120233 ◽

2019 ◽

Vol 11 (12) ◽

pp. 233

Author(s):

Marwa Hamdani ◽

Khouloud Krichen ◽

Mohamed Chaieb

Keyword(s):

Functional Traits ◽

Leaf Traits ◽

Perennial Grasses ◽

Arid Ecosystems ◽

Leaf Trait ◽

Grassland Species ◽

Dimensional Shrinkage ◽

Potential Link ◽

Dehydration Avoidance ◽

Stipa Lagascae

Aims of the study: The most important trends of the current climate variability is the scarcity of rains that affects arid ecosystems. The aim of this study was to explore the variability of leaf functional traits by which grassland species survive and resist drought and to investigate the potential link between resource use efficiency and water scarcity resistance strategies of species. Methods: Three grasses (Cenchrus ciliaris (C4), Stipa parviflora and Stipa lagascae (C3)) were established in a randomized block consisting of eleven replications. The seedlings were kept under increasing levels of water stress. In addition to their functional leaf traits, the rate of water loss and dimensional shrinkage were also measured. Key Results: Thicker and denser leaves, with higher dry matter contents, low specific leaf area and great capacity of water retention are considered among the grasses’ strategies of dehydration avoidance. Significant differences between the means of the functional traits were obtained. Furthermore, strong correlations among leaf traits were also detected (Spearman’s r exceeding 0.8). Conclusions: The results provide evidence that the studied grasses respond differently to drought by exhibiting a range of interspecific functional strategies that may ameliorate the resilience of grassland species communities under extreme drought events.

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