Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (15): 2914-2930.doi: 10.3864/j.issn.0578-1752.2024.15.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Identification of Candidate Genes Controlling SSCLD by Utilizing High-Generation Segregating Populations RNA-seq

CHEN WenJie(), CHEN Yuan, WEI QingYuan, TANG FuYue, GUO XiaoHong, CHEN ShuFang, QIN XiaYan, WEI RongChang, LIANG Jiang()   

  1. Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Nanning 530007
  • Received:2024-01-21 Accepted:2024-03-18 Online:2024-08-01 Published:2024-08-05
  • Contact: LIANG Jiang

Abstract:

Objective】 Severe SSCLD can lead to about 40% yield reduction of soybean. In this study, candidate genes associated with controlling SSCLD were identified by HGRNA-seq technology to provide data support for revealing the molecular mechanisms of SSCLD.【Method】Two parents with SSCLD resistance difference and their derived F2:7 lines were used as the experimental materials. Two parents and 12 F2:7 lines (7 crinkled leaves and 5 normal leaves) were separately subjected to re-sequenced and transcriptome sequencing. Mixed pool method was carried out for gene localization by using SNP/InDel data from the parents and their progenies. GO and KEGG functional annotation and enrichment analysis was carried out by using differentially expressed genes (DEGs) from RNA-seq. 7 KASP molecular markers were developed in the vicinity of localization interval, and 230 F2 populations were used to construct a localized linkage map to verify the localization results of the transcriptome data. Candidate genes controlling SSCLD were screened by combining gene mapping and transcriptome analysis.【Result】The gene controlling SSCLD named CL12 was located on chromosome 12 within a 1 473 464 bp interval by using mixed pool method, ranging from 39 231 651 bp to 40 705 115 bp. At the same time, the gene was localized in the 1 205 020 bp interval from 39 743 275 to 40 948 295 bp by using the F2 population, which was basically consistent with the results of the mixed-pool method. The GO annotation results showed that the metabolic processes included immune system processes and responses to stimuli, and cellular components were mainly related to membranes, etc. The KEGG annotation results showed that the biosystem pathways mainly included plant-pathogen interaction and environmental adaptation, etc. GO-enriched DEGs were mainly related to the activity of transmembrane receptor proteins, protein phosphorylation, and signaling receptors, etc., KEGG enriched DEGs were mainly related to plant-pathogen interaction and MAPK signaling pathway. Combined with the characteristics of the causal factors of SSCLD, genes within the candidate interval associated with disease resistance which had non-synonymous mutations in the coding exons, or showed differential expression were selected as candidate genes for SSCLD resistance. GLYMA_12G223100, GLYMA_12G223900, GLYMA_12G224100, GLYMA_12G231800 and GLYMA_12G233000 were finally identified as the candidate genes controlling SSCLD by qRT-PCR.【Conclusion】HGRNA-seq realized the combination of RNA-seq and BSA-seq, and successfully mined the candidate genes controlling SSCLD.

Key words: soybean, transcriptome, crinkle leaf disease, localization, molecular markers, second generation sequencing

Fig. 1

Field performance of F2:7 lines crossed from Y2017-1 and GC8 A and C: Homozygous crinkle leaf plant; B: Heterozygous crinkle leaf plant"

Table 1

The information of KASP markers used for genotyping 230 F2 crinkle leaf plants"

标记 Markers Primer_AlleleFAM (5′-3′) Primer_AlleleHEX (5′-3′) Primer_Common (5′-3′) AlleleFAM AlleleHEX
Chr.12_38720327 gaaggtgaccaagttcatgctaaagcatgctttaatattttggA gaaggtcggagtcaacggattaagcatgctttaatattttggG GCAATTGAAAACATAAGTCACGCCTAC A G
Chr.12_39553364 gaaggtgaccaagttcatgcttaaatcgtgtttcttttcctcctgC gaaggtcggagtcaacggatttgtaaatcgtgtttcttttcctcctgT CCCAACGGCTGCAATGGTC C T
Chr.12_39643002 gaaggtgaccaagttcatgctatggttggaccagacaggtaaggG gaaggtcggagtcaacggattatggttggaccagacaggtaaggA CTCTTTGCGCTGCTCGTCATTACTC G A
Chr.12_39743275 gaaggtgaccaagttcatgctgggagtccttgttatgtattatgatggC gaaggtcggagtcaacggattgagggagtccttgttatgtattatgatggT ATCCCCTAAGAAGTTGATACCACAT C T
Chr.12_40239112 gaaggtgaccaagttcatgctggaggcgactaaaattgtttccaaT gaaggtcggagtcaacggattggaggcgactaaaattgtttccaaC AAATTAGCCAAACACGCATGGTTCA T C
Chr.12_40443647 gaaggtgaccaagttcatgctccgaattgtgttttaagtcatatcT gaaggtcggagtcaacggattccgaattgtgttttaagtcatatcC GCAATATCAAGAATGAAACTTCT T C
Chr.12_40948295 gaaggtgaccaagttcatgctattgaaccatgttagcacagcagtT gaaggtcggagtcaacggattattgaaccatgttagcacagcagtA TAACAGAATGCTAACTTGTGATACT T A

Table 2

The statistics table of transcriptome and two parents sequencing and quality control data"

样本
Sample
过滤得到的reads数
Clean reads
过滤后的总碱基数
Clean bases
Q30
(%)
GC含量
GC content (%)
定位到基因组总Reads占比
Mapped Reads radio (%)
GC8 37329976 11235520244 91.72 35.15 99.54
Y2017-1 36749923 11054768304 92.28 35.69 98.64
C_10 48149604 7164122179 96.23 45.71 94.20
C_11 47618902 7090388779 96.57 45.95 94.19
C_18 45335046 6734925207 96.65 45.6 95.18
C_23 49603440 7381504895 96.56 46.14 95.12
C_24 49929876 7430549886 96.52 45.69 95.35
C_3 41997550 6249241100 96.59 45.94 94.70
C_6 45105078 6703705471 96.55 46.07 94.78
N_1 48155648 7150543340 96.44 45.87 95.00
N_3 44567696 6617278005 96.44 45.86 93.82
N_5 47817526 7091029900 96.66 46.07 94.92
N_6 42285914 6296598949 95.26 45.57 94.52
N_7 40742934 6065420513 96.49 46.24 94.91

Table 3

Distribution of SNP/InDel and genes with SNP/InDel in the transcriptome on soybean chromosomes"

染色体
Chromosome
长度
Length
(bp)
来自GC8
From GC8
来自Y2017-1
From Y2017-1
相同位点
Same site
杂合位点
Hybridization site
SNP/InDel数
No. of SNP/ InDel site
位点总数
Total numbers of SNP/InDel site
纯合率
Purity ratio (%)
标记密度
Density of SNP/ InDel (SNP/Mb)
Chr.1 57932355 150 285 607 11 435 1053 98.96 7.70
Chr.2 50400358 143 218 616 10 361 987 98.99 7.36
Chr.3 46951866 68 334 1107 159 402 1668 90.47 11.95
Chr.4 51203389 159 156 602 26 315 943 97.24 6.66
Chr.5 42274530 299 1 854 239 300 1393 82.84 12.75
Chr.6 50945864 326 217 1196 54 543 1793 96.99 11.72
Chr.7 44949256 479 125 1091 188 604 1883 90.02 17.62
Chr.8 47227184 119 501 820 476 620 1916 75.16 23.21
Chr.9 50572668 339 201 984 284 540 1808 84.29 16.29
Chr.10 51638687 84 229 616 70 313 999 92.99 7.42
Chr.11 39643745 35 277 584 27 312 923 97.07 8.55
Chr.12 41531199 106 77 690 131 183 1004 86.95 7.56
Chr.13 45225048 159 88 1399 422 247 2068 79.59 14.79
Chr.14 49893278 240 176 679 103 416 1198 91.40 10.40
Chr.15 53754295 84 271 955 185 355 1495 87.63 10.05
Chr.16 38112070 637 191 1193 157 828 2178 92.79 25.84
Chr.17 41740656 24 425 597 23 449 1069 97.85 11.31
Chr.18 58286270 404 357 1975 159 761 2895 94.51 15.78
Chr.19 51272880 94 94 924 25 188 1137 97.80 4.15
Chr.20 47846026 323 14 776 16 337 1129 98.58 7.38
总计/平均
Total/mean
961401624 4272 4237 18265 2765 8509 29539 91.61 11.73

Fig. 2

Scatter plot of expression differences"

Table 4

Distribution of differentially expressed genes on different chromosomes of soybean in the transcriptome"

染色体
Chromosome
DEGs数 No. of DEGs 总计
Total
有SNP/InDel的基因 No. of genes with SNP/InDel sites
上调 Up 下调 Down 上调 Up 下调 Down
Chr.1 53 9 62 26 2
Chr.2 45 3 48 19 1
Chr.3 48 2 50 23 1
Chr.4 42 5 47 9 1
Chr.5 45 6 51 17 1
Chr.6 74 6 80 46 3
Chr.7 55 3 58 22 0
Chr.8 73 3 76 26 2
Chr.9 53 6 59 20 2
Chr.10 48 5 53 8 3
Chr.11 44 5 49 12 3
Chr.12 39 5 44 16 2
Chr.13 79 5 84 36 2
Chr.14 44 5 49 22 3
Chr.15 56 0 56 25 1
Chr.16 96 3 99 76 1
Chr.17 44 2 46 16 0
Chr.18 49 5 54 33 3
Chr.19 31 2 33 19 1
Chr.20 37 4 41 11 0
其他Others 8 1 9 6 0
总计Total 1063 85 1148 488 32

Fig. 3

Index correlation analysis of SNP/InDel A: Index values of the proportion of GC8 genotype plants in the progeny of the crinkle leaf type; B: Index values of the proportion of GC8 genotype plants in the progeny of the normal leaf type; C: Distribution of delta index values on chromosomes"

Fig. 4

Expression of four genes with significant expression differences within the localization interval in 12 soybean samples"

Fig. 5

Results of localized linkage map construction and crinkle leaf gene localization using 230 F2 crinkle leaf isolates"

Fig. 6

GO (A) and KEGG (B) functional annotation analysis of differential expressed genes"

Fig. 7

GO items (A) and KEGG (B) pathways significantly enriched for differential expressed genes"

Table 5

Primer sequences for qRT-PCR analysis of four DEGs genes in transcriptome sequencing within the localization interval"

基因编号
Gene ID
标记
Marker
正向引物
Forward primer (5′-3′)
反向引物
Reverse primer (5′-3′)
退火温度
Tm (℃)
GLYMA_12G223900 qPCR-12G223900 TGTGTAGTGGCTTGTCATAT CTTAGTCTTATGGAGCAATCAC 60
GLYMA_12G224000 qPCR-12G224000 ATTGATGTTGGTGCTTCTTG TGAATGTGTTGGTGCTTCTA 60
GLYMA_12G224100 qPCR-12G224100 CATCAACCCAACTCACTCAA GTGGCAACATAAACTCTTGT 60
GLYMA_12G233000 qPCR-12G233000 GCTTCAACCGATCAACTTAT CCACCATACATATAGCAAGC 60

Fig. 8

Validation of the expression of four DEGs genes in transcriptome sequencing within the localization interval ns: No significant difference, *: Significant difference (P<0.05)"

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