尾细桉生长和木材密度关联SNP挖掘与候选基因定位

doi:10.12302/j.issn.1000-2006.202004003

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南京林业大学学报（自然科学版） ›› 2021, Vol. 45 ›› Issue (4): 143-150.doi: 10.12302/j.issn.1000-2006.202004003

尾细桉生长和木材密度关联SNP挖掘与候选基因定位

朱显亮(), 周长品, 贾翠蓉, 翁启杰, 李发根^*()

中国林业科学研究院热带林业研究所, 热带林业研究国家林业和草原局重点实验室,广东广州 510520

收稿日期:2020-04-04 接受日期:2020-09-26 出版日期:2021-07-30 发布日期:2021-07-30
通讯作者: 李发根
基金资助:
广东省自然科学基金项目(2020A1515010974);中国林科院基本科研业务费专项(CAFYBB2017MA006)

Association of SNP loci and candidate genes for growth and wood density in Eucalyptus urophylla × E. tereticornis

ZHU Xianliang(), ZHOU Changpin, JIA Cuirong, WENG Qijie, LI Fagen^*()

Key Laboratory of National Forestry and Grassland Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China

Received:2020-04-04 Accepted:2020-09-26 Online:2021-07-30 Published:2021-07-30
Contact: LI Fagen

摘要/Abstract

摘要：

【目的】生长和木材基本密度是桉树的重要经济性状,挖掘其候选功能基因可为桉树遗传改良提供参考。【方法】以尾叶桉(Eucalyptus urophylla)和细叶桉(Eucalyptus tereticornis) F1全同胞子代试验林为研究对象,测定其8年生树高、胸径和木材基本密度,开展表型遗传分析。筛选极端表型个体,利用测序分型(GBS)开发SNP标记进行关联分析。挖掘与树高、胸径和木材基本密度关联的SNP位点,并进行候选基因初步定位。【结果】尾细桉F1子代树高、胸径与木材基本密度间的表型变异系数为7.51%~26.19%,生长性状与木材基本密度显著正相关。利用GBS获得了覆盖全基因组的15 185个SNP位点,关联分析共鉴定111个与生长和木材基本密度显著关联的SNP,其中2号染色体上检测到强烈的生长性状关联信号。定位40个与生长和木材基本密度相关候选基因,共富集在52个GO terms,基因功能注释分析表明其功能主要与植物抗逆性、生物与非生物胁迫、转录因子家族等相关。【结论】本研究获得了一批与尾细桉生长和材性性状关联的SNP位点和候选基因,并进行了树高、胸径及木材基本密度候选基因初步定位,挖掘的与抗逆性相关的基因可能在树木的生长和木材形成中发挥重要作用。

关键词: 尾细桉, 测序分型, 单核苷酸多态性(SNP), 表型性状, 关联分析, 候选基因

Abstract:

【Objective】Growth and basic wood density are important economic traits of Eucalyptus; thus, searching for candidate genes will facilitate the genetic improvement in this genus.【Method】The interspecific full-sib family of E. urophylla and E. tereticornis was employed in this study. In addition, the correlation between the growth traits (height, dia-meter) and basic wood density of eight-year-old trees was investigated. The extreme phenotypes for each trait were screened for genotyping by sequencing (GBS) and developing SNP loci. Subsequently, association analyses of phenotypes and SNP loci were performed. Finally, SNP loci associated with the growth traits and basic wood density of E. urophylla × E. tereticornis were identified; candidate genes for these related traits were also identified. 【Result】① The phenotypic coefficient of variation ranged from 7.51% to 26.19% among the values of height, diameter, and basic wood density, while a significant positive correlation between the growth traits and basic wood density was found. ② A total of 15 185 whole-genome SNP loci were developed, and a total of 111 SNPs were identified as being significantly associated with growth and basic wood density; among which, strong association signals for diameter were detected on chromosome No.2. ③ In addition, 40 candidate genes related to the growth and basic wood density were identified, which were enriched in 52 GO terms. Gene annotation indicated that the candidate genes were mainly involved in plant stress resis-tance, biotic and abiotic stress, and transcription factor families.【Conclusion】In this study, a new set of SNP loci rela-ted to the growth traits and wood properties of E. urophylla × E. tereticornis were obtained, and dozens of candidate genes were identified. Our results suggest that genes related to stress resistance may play an important role in tree growth and wood formation. This information provides valuable genetic resources for research on Eucalyptus breeding.

Key words: Eucalyptus urophylla×E. tereticornis, genotyping by sequencing, single nucleotide polymorphism(SNP), phenotypic character, association analysis, candidate genes

中图分类号:

S781

朱显亮,周长品,贾翠蓉,等. 尾细桉生长和木材密度关联SNP挖掘与候选基因定位[J]. 南京林业大学学报（自然科学版）, 2021, 45(4): 143-150.

ZHU Xianliang, ZHOU Changpin, JIA Cuirong, WENG Qijie, LI Fagen. Association of SNP loci and candidate genes for growth and wood density in Eucalyptus urophylla × E. tereticornis[J].Journal of Nanjing Forestry University (Natural Science Edition), 2021, 45(4): 143-150.DOI: 10.12302/j.issn.1000-2006.202004003.

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性状traits	H/m	D/cm	ρ /(g·cm^-3)
总体平均值±标准误population mean ± SE	19.73±0.12	15.62±0.15	0.504 86±0.001 36
变异范围range	7.50~24.70	6.20~26.00	0.310 00~0.580 00
极低个体平均值mean of extreme low individuals	12.42^***	9.40^***	0.422 40^***
极高个体平均值mean of extreme high individuals	23.82^***	23.48^***	0.565 98^***
偏度kurtosis	-0.92	0.07	-1.00
峰度skewness	0.21	-0.74	1.71
变异系数/% coefficient of variation	17.38	26.19	7.51

指标 index	H	D	ρ
H	1
D	0.792^**	1
ρ	0.559^**	0.480^**	1

无性系号 clones No.	原始序列数 raw reads	高质量序列数 clean reads	Q30/%	GC占比/% GC rate	测序覆盖度 average depth	比对率/% percentage of mapped reads
244	6 747 598	6 284 629	89.9	41.5	1.27	97.5
269	7 238 380	6 696 361	90.0	41.5	1.36	97.4
414	7 451 706	6 361 698	86.7	41.8	1.37	96.6
436	7 339 146	6 788 388	90.8	41.7	1.37	97.3
446	5 568 416	5 161 141	90.5	40.3	1.09	97.8
453	8 922 734	8 186 482	88.7	41.7	1.69	97.6
503	7 973 560	7 304 918	90.2	41.0	1.50	97.4
511	6 690 676	5 931 829	88.1	41.9	1.21	96.8
536	10 247 840	9 331 703	88.5	42.1	1.91	97.1
542	9 133 484	8 361 043	88.6	42.6	1.71	97.3
591	14 002 206	12 404 893	90.3	41.8	2.69	97.7
630	10 350 070	9 126 378	90.2	42.2	1.97	97.7
676	9 337 480	8 687 413	92.3	40.9	1.75	97.1
766	6 951 718	6 095 388	88.7	42.1	1.29	97.3
773	7 653 990	6 731 562	88.7	42.0	1.46	97.5
818	6 837 196	5 686 663	88.7	41.3	1.28	96.5
889	6 230 868	5 269 415	88.4	41.5	1.14	96.4
906	6 045 060	4 966 451	85.6	42.0	1.06	96.2
931	8 831 366	8 082 888	90.4	42.0	1.65	97.4
1034	6 275 350	5 725 428	90.4	41.5	1.17	96.7
1037	9 039 954	8 386 655	92.0	41.0	1.69	97.1

性状 traits	标记 loci	P	染色体 chromosome	SNP位置 SNP position
H	R1_nn_np_2206	5.54×10^-7	1	31 185 986
H	R2_nn_np_1021	8.81×10^-7	5	73 028 798
H	R1_nn_np_265	6.94×10^-7	6	51 359 043
D	R1_lm_ll_1464	8.56×10^-9	2	16 463 419
D	R2_lm_ll_2467	1.83×10^-8	2	36 421 398
D	R2_lm_ll_3115	2.06×10^-8	2	27 860 410
D	R1_lm_ll_435	3.10×10^-8	2	21 688 358
D	R2_lm_ll_1597	3.10×10^-8	2	26 162 008
D	R1_lm_ll_2005	3.10×10^-8	2	22 047 469
D	R2_hk_hk_69	4.01×10^-7	2	7 731 971
D	R2_lm_ll_1030	2.20×10^-8	7	19 329 014
D	R1_hk_hk_233	3.58×10^-7	11	7 051 289
D	R1_hk_hk_24	4.10×10^-7	11	2 330 164
D	R2_lm_ll_2776	2.20×10^-8	none	-
D	R2_lm_ll_2539	2.56×10^-8	none	-
D	R1_lm_ll_1496	3.10×10^-8	none	-
ρ	R1_nn_np_3087	4.46×10^-6	4	32 583 746
ρ	R1_nn_np_2972	4.46×10^-6	7	48 651 807
ρ	R2_lm_ll_2539	2.47×10^-6	none	-

尾细桉生长和木材密度关联SNP挖掘与候选基因定位

Association of SNP loci and candidate genes for growth and wood density in Eucalyptus urophylla × E. tereticornis

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染色体号 chromosome No.	关联SNPs associated SNPs			候选基因 candidate genes
染色体号 chromosome No.	H	D	ρ	H	D	ρ
1	10	0	0	3	0	0
2	0	10	3	0	1	0
3	1	2	1	0	1	0
4	4	1	1	3	0	1
5	7	2	0	3	0	0
6	17	4	3	11	1	1
7	2	1	11	1	0	9
8	3	0	0	2	0	0
9	13	0	0	5	0	0
10	1	0	0	0	0	0
11	0	2	0	0	1	0
SCA	4	3	1	0	0	0
none	4	6	2	-	-	-
小计subtotal	66	31	22	28	4	10
总计total			111^a			40^b

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