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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (10): 1557-1565.doi: 10.3724/SP.J.1006.2020.04007


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 Online:2020-10-12 Published:2020-04-27
  • Contact: Jia-Na LI E-mail:hjjian518@swu.edu.cn;354011524@qq.com;ljn1950@swu.edu.cn
  • Supported by:
    National Key Research and Development Program of China(2018YFD0100504-05);Special Project of Chongqing People’s Livelihood(cstc2016shms-ztzx80020)


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

Table 1

List of primer sequences for candidate genes"

基因Gene 引物序列Primer sequence (5°-3°)

Table 2

Phenotypic variation of chlorophyll content in natural population"

Mean ± SD
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

Fig. 1

Frequency distribution of chlorophyll content in leaves of B. napus"

Fig. 2

Quantile-quantile plot for six models of chlorophyll contents"

Fig. 3

Manhattan plots of association analysis using the optimal model of chlorophyll contents"

Table 3

Summary of significant SNPs for chlorophyll content by using the best model"

环境Environment 位点
lg (P-value)
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
lg (P-value)
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

Table 4

Candidate genes for chlorophyll content"

Gene name
Physical position
Homologs in A. thaliana
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
Gene name
Physical position
Homologs in A. thaliana
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)

Fig. 4

Expression profiles of chlorophyll content candidate genes in leaves of B. napus using qRT-PCR"

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