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

doi:10.12302/j.issn.1000-2006.202004003

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2021, Vol. 45 ›› Issue (4): 143-150.doi: 10.12302/j.issn.1000-2006.202004003

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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 E-mail:1099418037@qq.com;lifagen@caf.ac.cn

Abstract

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

CLC Number:

S781

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, 2021, 45(4): 143-150.

Figures/Tables 9

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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	-

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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