Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq

doi:10.16420/j.issn.0513-353x.2024-0315

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (6): 1505-1518.doi: 10.16420/j.issn.0513-353x.2024-0315

• Genetic & Breeding?Germplasm Resources?Molecular Biology • Previous Articles Next Articles

Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq

LI Ziyan¹^,², CHEN Weixi¹^,², LI Zihan¹^,², LI Yin¹^,², LIANG Fengming⁵, ZENG Xiangli⁵, JIAN Hongju¹^,²^,³^,⁴^,^*(), and LÜ Dianqiu¹^,²^,³^,⁴^,^*()

¹ Integrative Science Center of Germplasm Creation in Western China（Chongqing）Science City，Southwest University，Chongqing 400715，China
² College of Agronomy and Biotechnology，Southwest University，Chongqing 400715，China
³ Engineering Research Center of South Upland Agriculture，Ministry of Education，Southwest University，Chongqing 400715，China
⁴ Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops，Southwest University，Chongqing 400715，China
⁵ Wuxi County Shuguang Agricultural Science and Technology Development Co.，Ltd.，Chongqing 405899，China

Received:2025-01-20 Revised:2025-03-06 Online:2025-06-20 Published:2025-06-20
Contact: JIAN Hongju, and Lü Dianqiu

Abstract

Abstract:

In this study，early maturing cultivars‘Zaodabai’‘Zhongshu5’‘Eshu3’，middle late maturing cultivar ‘Atlantic’and late maturing cultivar‘Qingshu 9’were used to analyze the relationship between potato apical meristem development and tuberization time，Zaodabai and Qingshu 9 were also taken to study the function of differentially expressed genes as well as the possible regulatory pathways involved by RNA-Seq. Results showed that the apical meristem turned to reproductive growth earlier in early maturing cultivars than late maturing cultivars. A total of 2 842 differentially expressed genes were identified in transcriptome sequencing，85% of which related to hormones were concentrated in hormone signal transduction pathways and showed rich expression differences，especially in IAA，ABA，JA and other pathways. Besides，a total of 127 differentially expressed transcription factor genes were identified，distributed in 35 transcription factor families. GO and KEGG enrichment analysis showed that differentially expressed genes were mainly concentrated in photosynthesis，hormone response，plant circadian rhythm，starch and sucrose metabolism，and plant hormone signal transduction. The 20 candidate genes that may affect the early and late tuberization of potato were selected for qRT-PCR verification. The genes involved in the circadian rhythm pathway，FT and HY5，were highly expressed in Zaodabai. Genes involved in the starch and sucrose metabolic pathway，BGLU17，CWIN2 and GH9B13 were highly expressed in Zaodabai. GH3，RD22，HB16 and CYP74A involved in plant hormone signal transduction or anabolism were highly expressed in Zaodabai，while IAA17，MES1 and RCA were highly expressed in Qingshu 9. In addition，GRP3 which highly expressed in Zaodabai may also affect tuberization time. These genes may play a role in potato by regulating photoperiodic response，hormone signal transduction，sucrose level，etc.，thus affecting potato tuberization time.

Key words: potato, transcriptome sequencing, maturation, apical meristem, differential expressed gene, photoperiod, hormone, sucrose

LI Ziyan, CHEN Weixi, LI Zihan, LI Yin, LIANG Fengming, ZENG Xiangli, JIAN Hongju, and LÜ Dianqiu. Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq[J]. Acta Horticulturae Sinica, 2025, 52(6): 1505-1518.

Figures/Tables 8

References 45

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名称Name	基因ID Gene ID	正向引物（5′-3′）Forward primer	反向引物（3′-5′）Reverse primer
GH3	Soltu.DM.10G002010	TGAAGCCATTCTCTGCCTAGACTC	AGCCAACACGAACGACTTCTCTG
SAUR79	Soltu.DM.08G022860	GGTAGCAATCTTGACAAGGCGATG	TTCCTTTCCCACCAGCACAGTTAC
IAA17	Soltu.DM.03G035030	GATGGAGACTGGATGCTTGTTGGA	CCTCCGTGCTCTTCATCAACCTAA
RD22	Soltu.DM.08G017220	GGTGTCTATGGTGGGTGCTGATG	ATAGGCTTGTCTCCAGGCTTAACG
HB16	Soltu.DM.11G003380	GGTTGGTTGTTCATCTCCGTTGA	TGTTGTTGTTGTTGTTGACGAAGG
CYP74A	Soltu.DM.10G003720	TGGATTGGAACATCAGGACCTAGT	ACCACAGACTTAACAAGAGGCATT
MES1	Soltu.DM.02G008550	CCTGAAGAGCCTCGGACATCCA	GGTCTCACCAACGACGATGCTAAT
MES3	Soltu.DM.01G048330	TGCCAATCCTCCAACAACCTTCAT	GTAGTAGCCAGTGCCCAGTCCT
RCA	Soltu.DM.10G023180	ACTCACCATCCTGTCTTGTCATCA	ATCCATCCAGCGTGTTGTCCAG
GIM2	Soltu.DM.08G001760	ACTTGGTATGCCACCTCATTCAGA	TCGAGATGGTCGCCGGTATTG
FT	Soltu.DM.05G026370	CAAGCCCAAGCGACCCTAACTT	CGTAGGTGTTGGATTCTCGTAGCA
COP1	Soltu.DM.11G001010	AGGAGGAAGAGGAAGAGGAAGAGG	AACTATGTCCACACGCCGTTAGAA
HY5	Soltu.DM.08G011730	TGCCGCTAGTTCACTACCTTCAAG	ACATCGTTCCCGTCGCTTCTC
GRP3	Soltu.DM.09G030440	ATTATGGAGGCGGCTATGGTAAGG	AGTCTGGGCAGCCACATATTCTTC
RBCS3B	Soltu.DM.02G025840	AGGTCTTGGCTGAGGTGGAGGA	AACTGATGCACTGCACTTGACGAA
GH9B13	Soltu.DM.09G023670	ACGAGCGATCAGATTACGAGCAAT	TGAGCAAGGTAAGTGAGTGTTCCA
BGLU45	Soltu.DM.07G024580	ACAAGGTGGAACGATAGGAATGGT	AGGATCAAGAAGCCAGGCAACAT
ADG2	Soltu.DM.01G024440	GCAGGTGAGGCTAAGTTGAAGGAT	CCCATTGGAACGGCAGGCTTA
BGLU17	Soltu.DM.10G010830	GTCGGCTCCCAAGATTCACAGTT	CAGCATGATTGTCAGTGGTGTAGC
CWIN2	Soltu.DM.10G025030	ATGTTGGTTGGGTCAGGATGGTT	CCGTCAACTGAATGAAGTGGATGT

名称Name	基因ID Gene ID	正向引物（5′-3′）Forward primer	反向引物（3′-5′）Reverse primer
GH3	Soltu.DM.10G002010	TGAAGCCATTCTCTGCCTAGACTC	AGCCAACACGAACGACTTCTCTG
SAUR79	Soltu.DM.08G022860	GGTAGCAATCTTGACAAGGCGATG	TTCCTTTCCCACCAGCACAGTTAC
IAA17	Soltu.DM.03G035030	GATGGAGACTGGATGCTTGTTGGA	CCTCCGTGCTCTTCATCAACCTAA
RD22	Soltu.DM.08G017220	GGTGTCTATGGTGGGTGCTGATG	ATAGGCTTGTCTCCAGGCTTAACG
HB16	Soltu.DM.11G003380	GGTTGGTTGTTCATCTCCGTTGA	TGTTGTTGTTGTTGTTGACGAAGG
CYP74A	Soltu.DM.10G003720	TGGATTGGAACATCAGGACCTAGT	ACCACAGACTTAACAAGAGGCATT
MES1	Soltu.DM.02G008550	CCTGAAGAGCCTCGGACATCCA	GGTCTCACCAACGACGATGCTAAT
MES3	Soltu.DM.01G048330	TGCCAATCCTCCAACAACCTTCAT	GTAGTAGCCAGTGCCCAGTCCT
RCA	Soltu.DM.10G023180	ACTCACCATCCTGTCTTGTCATCA	ATCCATCCAGCGTGTTGTCCAG
GIM2	Soltu.DM.08G001760	ACTTGGTATGCCACCTCATTCAGA	TCGAGATGGTCGCCGGTATTG
FT	Soltu.DM.05G026370	CAAGCCCAAGCGACCCTAACTT	CGTAGGTGTTGGATTCTCGTAGCA
COP1	Soltu.DM.11G001010	AGGAGGAAGAGGAAGAGGAAGAGG	AACTATGTCCACACGCCGTTAGAA
HY5	Soltu.DM.08G011730	TGCCGCTAGTTCACTACCTTCAAG	ACATCGTTCCCGTCGCTTCTC
GRP3	Soltu.DM.09G030440	ATTATGGAGGCGGCTATGGTAAGG	AGTCTGGGCAGCCACATATTCTTC
RBCS3B	Soltu.DM.02G025840	AGGTCTTGGCTGAGGTGGAGGA	AACTGATGCACTGCACTTGACGAA
GH9B13	Soltu.DM.09G023670	ACGAGCGATCAGATTACGAGCAAT	TGAGCAAGGTAAGTGAGTGTTCCA
BGLU45	Soltu.DM.07G024580	ACAAGGTGGAACGATAGGAATGGT	AGGATCAAGAAGCCAGGCAACAT
ADG2	Soltu.DM.01G024440	GCAGGTGAGGCTAAGTTGAAGGAT	CCCATTGGAACGGCAGGCTTA
BGLU17	Soltu.DM.10G010830	GTCGGCTCCCAAGATTCACAGTT	CAGCATGATTGTCAGTGGTGTAGC
CWIN2	Soltu.DM.10G025030	ATGTTGGTTGGGTCAGGATGGTT	CCGTCAACTGAATGAAGTGGATGT

Screening Candidate Genes Controlling Potato Maturation Time Based on RNA-Seq

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