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作物学报 ›› 2020, Vol. 46 ›› Issue (10): 1557-1565.doi: 10.3724/SP.J.1006.2020.04007

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

用全基因组关联分析筛选甘蓝型油菜叶片叶绿素含量候选基因

荐红举1,2(), 霍强1,2(), 高玉敏1,2, 李阳阳1,2, 谢玲1,2, 魏丽娟1,2, 刘列钊1,2, 卢坤1,2, 李加纳1,2,*()   

  1. 1 西南大学农学与生物科技学院, 重庆 400715
    2 西南大学现代农业科学研究院, 重庆 400715
  • 收稿日期:2020-01-12 接受日期:2020-04-15 出版日期:2020-10-12 网络出版日期:2020-04-27
  • 通讯作者: 李加纳
  • 作者简介:荐红举, E-mail: hjjian518@swu.edu.cn;|霍强, E-mail: 354011524@qq.com
  • 基金资助:
    国家重点研发计划项目(2018YFD0100504-05);重庆市民生工程主题专项(cstc2016shms-ztzx80020)

Selection of candidate genes for chlorophyll content in leaves of Brassica napus using genome-wide association analysis

JIAN Hong-Ju1,2(), HUO Qiang1,2(), GAO Yu-Min1,2, LI Yang-Yang1,2, XIE Ling1,2, WEI Li-Juan1,2, LIU Lie-Zhao1,2, LU Kun1,2, LI Jia-Na1,2,*()   

  1. 1 College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    2 Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
  • Received:2020-01-12 Accepted:2020-04-15 Published:2020-10-12 Published online:2020-04-27
  • Contact: Jia-Na LI
  • Supported by:
    National Key Research and Development Program of China(2018YFD0100504-05);Special Project of Chongqing People’s Livelihood(cstc2016shms-ztzx80020)

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摘要：

提高油菜产量是保障国家粮油安全的重要举措。作物“源”“流”“库”理论表明, 充足的光合产物(源)是高产的前提, 而叶绿素是直接参与光合作用的物质, 因此, 选育高叶绿素含量的甘蓝型油菜是提高产量的重要途径。本课题组前期对全球收集的588份优异油菜种质资源进行5X重测序, 获得385,692个高质量SNP标记。利用SPAD-502叶绿素仪于2018—2019连续2年测定苗期完全伸展的叶片叶绿素总量, 结合获得的SNP标记进行全基因组关联分析(genome-wide association study, GWAS), 筛选与叶绿素含量显著关联的SNP位点。结果表明, 2018年鉴定到5个显著关联的SNP位点, 贡献率为5.51%~7.89%, 其中S6_3493805位点贡献率最大; 2019年检测到46个SNP位点, 贡献率为7.29%~10.34%, 其中S13_11413088位点贡献率最大。将显著关联SNP位点上下游各500 kb区间内的基因与参考基因组比对, 初步筛选出2022个油菜基因。将其基因序列在拟南芥基因组内进行BLAST比对, 结合前人已报道的拟南芥同源基因功能, 筛选到23个候选基因, 其中5个属于叶绿素合成途径同源基因。本研究结果为后续油菜叶片叶绿素含量的遗传改良奠定了基础。

关键词: 甘蓝型油菜, 叶绿素含量, 全基因组关联分析, 候选基因

Abstract:

Increasing rapeseed production is important to ensure the national food and oil security. According to the theory of crop source and sink, sufficient photosynthate (sources) is the premise of high yield, and chlorophyll is the important substance for photosynthesis. Therefore, breeding high chlorophyll content Brassica napus is an important way to ensure high yield. In our previous study, 588 excellent germplasm resources collected worldwide were re-sequenced with 5x and 385,692 high-quality SNP markers were obtained. SPAD-502 chlorophyll meter was used to measure the total chlorophyll content of mature leaves in 2018-2019. Genome wide association study (GWAS) was conducted to screen SNP sites significantly related to chlorophyll content. Five SNP loci were identified in 2018, with a contribution rate of 5.51%-7.89%, of which S6_3493805 had the largest contribution. 46 SNP loci were detected in 2019, with a contribution rate of 7.29%-10.34%, of which S13_11413088 had the largest contribution. In total, 2022 rapeseed genes were screened out by comparing the reference genome with genes in the regions of the 500 kb before and after the SNP. Based on the function of Arabidopsis homologous genes previously reported, screened 23 candidate genes, among which five were homologous genes in chlorophyll synthesis pathway. These results lay a foundation for the genetic improvement of chlorophyll content in leaves of B. napus in future.

Key words: Brassica napus, chlorophyll content, GWAS, candidate genes

表1

候选基因引物"

基因Gene 引物序列Primer sequence (5°-3°)
BnaA04g00600D F: AAATGTCGTTGAGGAATTACGC; R: TGAATGATATACGTCAGCACCA
BnaC09g54390D F: AAGGAGCTAACACAATGACTGA; R: GGTATCATCACAGGTAACCCAT
BnaC03g18820D F: AATCATGTTTCCATTAGCCACG; R: CATTACCACCGTTGAAAACCAA
BnaC06g24160D F: AATGTTGCGCATTATCTTCCTC; R: TGTTTGTAGTGTTTCCAGGAGT
BnaC07g39280D F: AGAAAACGATGCTTATGCTGAC; R: CATAGCTGCAGAGATATCGCTA
BnaA04g00500D F: AGCTCATATACATTGTGGAGCA; R: TGCTGCTAGATTGGTCTAAGAG
BnaA02g24670D F: CTAATCGAATCAAGCCCTGTTG; R: GGTGAAAACGCAAAGAAATTGG
BnaC02g01240D F: CTCAAGGAGCTATTGGAATTGC; R: TATCCAGCAATAGGTGTACGAC
BnaC03g20950D F: CTTTATGGTGTTGGCCAAGTAC; R: AACTTTACCACGCCGTATTTTC
BnaC05g38600D F: GACTCTCTGAAGATACTGAGGC; R: ACTCTTGATCACCGTATACGTC
BnaA10g02050D F: GAGCTGGAACAATAACTCCTCT; R: CACAGTTTCTTTGCCTTCTCTG
BnaC05g10770D F: GAGTGTTCCTGATTGTATGCAC; R: AGATGTGCCAATCCAAAAGAAC
BnaC04g01850D F: GATAGGAACGGTGATGGTTTTG; R: TTCCGTCACGAAATTAAAACCC
BnaC02g25030D F: GTAAATGTGCCTGATGAGGTTG; R: TGAACAATCTCTTCGTCAAGGA
BnaA06g06000D F: GTCGCTGCTTAAACAGTTACAA; R: GAAACCCAACAAAGAGTGAACA
BnaA05g01720D F: GTTCACAACGTCAATGATCACA; R: GTGGCCCAAGAATCAAAGATTT
BnaC08g27000D F: GTTTCTGAACGAACAGGTTGAA; R: ATTTAAGCAGCAGCAGAAGTTC
BnaC09g05970D F: TTACTAGCTTGGCTCACACTAC; R: CGTTCTCATCAACAACACTCAG
BnaC09g05970D F: TTACTAGCTTGGCTCACACTAC; R: CGTTCTCATCAACAACACTCAG
BnaA01g20460D F: TTATCAAGCGTGCGAAGTAAAG; R: CGCGCTGATCTTAACCTAGTTA
BnaC08g27310D F: TTTGCTACCTGTTGAAAACGAC; R: TTATTCAACTGTGACAAAGCCG

表2

甘蓝型油菜叶绿素含量的表型数据统计分析"

性状
Trait		 环境
Environment		 均值±标准差
Mean ± SD		 范围
Range		 变异系数
CV (%)
叶绿素含量 2018 47.79±5.39 33.44-65.82 11.27
Chlorophyll content 2019 46.37±5.90 32.92-72.04 12.73

图1

甘蓝型油菜叶片叶绿素含量的频次分布"

图2

甘蓝型油菜叶绿素含量在各模型中的QQ图"

图3

甘蓝型油菜叶绿素含量在最佳模型中的曼哈顿图"

表3

最佳模型下叶绿素含量显著位点表"

环境Environment 位点
SNP		 染色体
Chr.		 位置
Position		 阈值
lg (P-value)		 贡献率
R2 (%)
2018 S1_12845378 A03 12,845,378 5.73 5.51
S6_3493805 A06 3,493,805 7.49 7.89
S6_3812220 A06 3,812,220 6.05 6.10
S10_4969863 A10 4,969,863 6.25 6.23
S14_37741561 C04 37,741,561 5.69 5.67
2019 S1_12688640 A01 12,688,640 6.39 8.42
S1_12540615 A01 12,540,615 6.10 8.24
S1_10570293 A01 10,570,293 5.93 8.51
S1_12628926 A01 12,628,926 5.86 8.28
S1_12540545 A01 12,540,545 5.84 7.67
S1_12540622 A01 12,540,622 5.83 7.66
环境Environment 位点
SNP		 染色体
Chr.		 位置
Position		 域值
lg (P-value)		 贡献率
R2 (%)
2019 S1_12628563 A01 12,628,563 5.79 9.76
S1_12568566 A01 12,568,566 5.78 7.55
S2_17839296 A02 17,839,296 6.91 9.73
S3_13514793 A03 13,514,793 5.73 7.72
S4_547942 A04 547,942 5.93 8.08
S8_16108365 A08 16,108,365 6.46 8.44
S8_16192480 A08 16,192,480 5.88 7.80
S8_16181282 A08 16,181,282 5.78 7.85
S8_16103637 A08 16,103,637 5.61 7.97
S8_16181355 A08 16,181,355 5.60 7.29
S9_10532790 A09 10,532,790 6.18 8.70
S10_14050715 A10 14,050,715 5.61 7.72
S12_20495602 C02 20,495,602 5.95 9.35
S12_22225349 C02 22,225,349 5.74 8.76
S13_11413088 C03 11,413,088 7.01 10.34
S13_11423629 C03 11,423,629 6.95 9.31
S13_11415175 C03 11,415,175 6.61 8.92
S13_11433444 C03 11,433,444 6.39 8.88
S13_11433450 C03 11,433,450 6.38 8.87
S13_9816561 C03 9,816,561 6.06 8.70
S13_48351338 C03 48,351,338 6.00 8.06
S13_11249216 C03 11,249,216 5.97 8.22
S14_7018412 C04 7,018,412 6.81 9.39
S14_1487936 C04 1,487,936 5.73 7.96
S14_5798300 C04 5,798,300 5.68 8.45
S14_36521995 C04 36,521,995 5.60 7.95
S15_6002527 C05 6,002,527 6.06 8.65
S16_24042352 C06 24,042,352 6.55 9.94
S16_14397036 C06 14,397,036 6.31 8.84
S16_25797577 C06 25,797,577 6.25 8.34
S16_25797598 C06 25,797,598 6.14 8.15
S16_25233735 C06 25,233,735 6.14 8.09
S16_25797558 C06 25,797,558 6.00 8.46
S16_25234451 C06 25,234,451 5.97 8.45
S16_25234262 C06 25,234,262 5.92 8.11
S16_25797570 C06 25,797,570 5.89 8.06
S16_25234230 C06 25,234,230 5.88 8.31
S18_31711591 C08 31,711,591 6.32 8.85
S18_28228959 C08 28,228,959 5.77 8.36
S19_32818852 C09 32,818,852 5.62 8.15

表4

叶绿素含量候选基因"

基因名字
Gene name		 物理位置
Physical position		 拟南芥同源基因
Homologs in A. thaliana		 功能注释
Functional annotation
BnaA01g20460D A01:12331065-1233745 AT3G48740 Nodulin MtN3 family protein
BnaA02g24670D A02:17989410-17990090 AT5G46780 VQ motif-containing protein
BnaA04g00500D A04:365464-366530 AT3G61890 Homeobox 12 (HB-12)
BnaA04g00600D A04:460722-461017 AT3G61640 Arabinogalactan protein 20 (AGP20)
BnaA05g01720D A05:984996-986020 AT2G40490 HEME2
BnaA06g06000D A06:3306811-3307795 AT1G10200 WLIM1
BnaA10g02050D A10:1025298-1027102 AT1G03630 Protochlorophyllide oxidoreductase C (POR C)
BnaC02g01240D C02:511615-513517 AT5G08280 Hydroxymethylbilane synthase (HEMC)
BnaC02g25030D C02:22402218-22403498 AT1G07440 NAD(P)-binding Rossmann-fold superfamily protein
BnaC03g18820D C03:9634933-9635479 AT2G33830 Dormancy/auxin associated family protein
BnaC03g20950D C03:11192271-11192876 AT2G37970 SOUL-1
BnaC04g01850D C04:1467437-1468078 AT2G41410 Calcium-binding EF-hand family protein
BnaC05g10770D C05:6194068-6195531 AT1G14480 Ankyrin repeat family protein
基因名字
Gene name		 物理位置
Physical position		 拟南芥同源基因
Homologs in A. thaliana		 功能注释
Functional annotation
BnaC05g38600D C05:37280225-37281849 AT3G14930 HEME1
BnaC06g24160D C06:25958767-25959390 AT1G72610 Germin-like protein 1 (GER1)
BnaC07g39280D C07:40238482-40239858 AT4G25080 Magnesium-protoporphyrin IX methyltransferase (CH LM)
BnaC08g27000D C08:28191454-28192970 AT3G56090 Ferritin 3 (FER3)
BnaC08g27310D C08:28357417-28358091 AT3G56360 Unknown protein
BnaC09g05970D C09:3640560-3642915 AT5G63570 Glutamate-1-semialdehyde-2,1-aminomutase (GSA1)
BnaC03g18980D chrC03:9831772-9832572 AT2G34430 Light-harvesting chlorophyll-protein complex II subunit B1 (LHB1B1)
BnaC02g25060D chrC02:22446772-22448037 AT1G78600 Light-regulated zinc finger protein 1 (LZF1)
BnaA04g00660D chrA04:488057-489279 AT3G61470 Photosystem I light harvesting complex gene 2 (LHCA2)
BnaA08g22200D chrA08:16221799-16222764 AT1G19150 Photosystem I light harvesting complex gene 6 (LHCA6)

图4

甘蓝型油菜叶片叶绿素含量候选基因定量验证"

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