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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (9): 2274-2284.doi: 10.3724/SP.J.1006.2022.14138

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

2b-RAD based maturity associated molecular marker identification in tetraploid potato (Solanum tuberosum L.)

HUI Zhi-Ming(), XU Jian-Fei, JIAN Yin-Qiao, BIAN Chun-Song, DUAN Shao-Guang, HU Jun, LI Guang-Cun, JIN Li-Ping*()   

  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences / Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
  • Received:2021-08-05 Accepted:2021-11-29 Online:2022-09-12 Published:2021-12-16
  • Contact: JIN Li-Ping E-mail:huizhiming@aliyun.com;jinliping@caas.cn
  • Supported by:
    New Potato Varieties Breeding of Agricultural Breeding Special Project of the Ningxia Hui Autonomous Region of China(2019NYYZ01-1)

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Abstract:

Potato maturity is a quantitative trait controlled by multiple genes and it is one of the major agronomic characteristics for selecting suitable varieties in different agro-ecological zones. In this study, the maturity of the segregating population derived from Zhongshu 18 (♀) × Zhongshu 5 (♂) was evaluated in 2018 and 2019. Respectively, 30 offsprings with extremely late or early maturity were selected and used to construct early and late maturing genomic pool. Three molecular markers (SCARA2-2, SCARA4-21, and SCARA5-16) linked to maturity were identified by simplified genome 2b-RAD (2b-restriction site-associated DNA) sequencing. The maturity phenotypic association rate of the three-marker-combination for the late and early maturity genotype verification reached 87.5% and 93.0%, respectively. Thus, these molecular markers are valuable for markers assisted selection in potato maturity breeding.

Key words: potato, maturity, 2b-RAD, molecular markers

Table 1

Published molecular markers of maturity traits in potato (Solanum tuberosum L.)"

分子标记
Molecular marker		 染色体(连锁群)
Chromosome
(linkage group)		 组合
Cross		 倍性
Ploidy		 群体
Population		 参考文献
Reference
GP179, GP76 Chr.V (Major QTL), Chr.VI (Minor QTL) G87D2.4.1 × I88.55.6
G87D2.4.1 × I86.102.1		 Diploid 109
29		 Oberhagemann et al. [21]
STM1100-STM1056, STM0028-STM3009, TM1057-STM0024 Chr.V, Chr.VI, Chr.VII, Chr.VIII G87D2.4.1 × I88.55.6 Diploid 113 Collins et al. [22]
GP21 Chr.V USW5337.3 × 77.2102.37 Diploid 67 Visker et al. [8]
STM3179 Chr.V 12601ab1 × Stirling Tetraploid 227 Bradshaw et al. [23]
分子标记
Molecular marker		 染色体(连锁群)
Chromosome
(linkage group)		 组合
Cross		 倍性
Ploidy		 群体
Population		 参考文献
Reference
GP21 Chr.III (Minor QTL), Chr.V (Major QTL) SH82-44-111 × CE51
DH84-19-1659 × dI88.55.6		 Diploid 227
300		 Visker et al. [24]
C51, C52, C53, C61, C62 Chr.V, Chr.VI S. phureja × S. tuberosum Diploid 205 Mal.osetti et al. [10]
GP186, BA47f2t7, CP113 Chr.V DG 83-1520 ×DG 84-195 Diploid 156 Sliwka et al. [25]
STM3179 Chr.V 12601ab1 × Stirling Tetraploid 227 Bradshaw et al. [11]
solcap_snp_c2_47609 Chr.V 12601ab1 × Stirling Tetraploid 190 Hackett et al. [12]
solcap_snp_c2_22986 Chr.V Jacqueline Lee × MSG227-2 Tetraploid 156 Massa et al. [13]
solcap_snp_c2_11605 Chr.V Rio Grande Russet ×
Premier Russet		 Tetraploid 162 Massa et al. [14]
SSR5-85-1, SCAR5-8 Chr.V Zhongshu 19 × Zhongshu 3 Tetraploid 221 Li et al. [9]
PM_Z_05 Chr.II, IV, V, VII, XI Longshu 8 × Zaodabai Tetraploid 192 Li et al. [26]

Table 2

Classification for potato maturity"

熟性等级
Maturity class		 生育期
Growth period (d)
1 ≤60
2 61-70
3 71-80
4 81-90
5 91-100
6 ≥101

Fig. 1

Identification of early-maturing marker SCAR5-8 and gene StCDF1.2 in early-maturing cultivar Zhongshu 5 and late-maturing cultivar Zhongshu 18 M1: DL2000; M2: marker III; P1: Zhongshu 5; P2: Zhongshu 18."

Fig. 2

Average results of investigation for maturity class of the population in 2018 and 2019"

Table 3

Characterization of sequencing data"

材料
Material		 原始reads
Clean reads		 高质量Reads
Enzyme reads		 百分数
Percentage (%)		 特异标签数
No. of uniq tags		 测序深度
Depth
中薯18号Zhongshu 18 58,046,070 51,631,527 88.95 121,964 162.5 ×
中薯5号Zhongshu 5 58,046,070 52,205,695 89.94 122,940 162.1 ×
极端晚熟混池Extremely late pool 58,046,070 52,383,011 90.24 128,108 158.2 ×
极端早熟混池Extremely early pool 58,046,070 53,881,077 92.82 127,564 161.1 ×
平均Mean 58,046,070 52,525,328 90.49 125,144 161.0 ×

Fig. 3

Distribution of tags on chromosomes (A) and unique tags for early and late maturity DNA pools (B) 0-80 M: physical distance of chromosomes (unit: M); Chr.1-Chr.12: 12 chromosomes of potato. A: left histogram: EPool is early maturity DNA pool, LPool is late maturity DNA pool; Right histogram: different color represents different number of unique tags; the figure represents the number of unique tags. B: on every chromosome, the up histogram represents the unique tags in early maturity pool, the middle histogram represents the unique tags in late maturity pool, the down histogram represents the absolute value of unique tags between early maturity pool and late maturity pool. Right histogram: Different color represents different number of unique tags. The figure represents the number of unique tags."

Fig. 4

Identification of SCARA5-16 in extreme early (A) and late (B) maturity progenies M: DL2000; P1: Zhongshu 5; P2: Zhongshu 18. A: number 27-51 for extreme early progenies; B: number 298-172 for extreme late maturity progenies."

Table 4

Verification of markers in extreme early and late progenies"

极端基因型
Extreme genotype		 样本总数(个)
Total number of samples		 标记名称
Marker name		 单标记表型符合率
Single coincidence rate (%)		 染色体
Chr.		 引物序列
Primer sequences(5°-3°)		 标记鉴定
Marker
identification		 标记联合使用表型符合率
Comprehensive coincidence rate (%)
极端晚熟
Extremely
late maturity		 30 SCARA2-2 56.7 2 F: ACAGCTCGGCGAGAAAACAG
R: TCAAGCAATTAGGGCGGTG		 阳性
Positive		 90.0
SCARA4-21 60.0 4 F: TCACTTTGGCGACCACACTT
R: CAGACCCGCTTACGCTAAGAT		 阳性
Positive
SCARA5-16 60.0 5 F: TTTTTGTGATCAGGGGCGG
R: TGCATTGCATCCTCCCAAC		 阳性
Positive
极端早熟
Extremely early maturity		 30 SCARA2-2 56.7 2 F: ACAGCTCGGCGAGAAAACAG
R:TCAAGCAATTAGGGCGGTG		 阴性
Negative		 96.7
SCARA4-21 60.0 4 F: TCACTTTGGCGACCACACTT
R: CAGACCCGCTTACGCTAAGAT		 阴性
Negative
SCARA5-16 76.7 5 F: TTTTTGTGATCAGGGGCGG
R: TGCATTGCATCCTCCCAAC		 阴性
Negative

Table 5

Associate analysis of maturity phenotyping and molecular marker test"

表型
Phenotype		 样本总数(个)
Total number of
samples		 标记名称
Marker name		 单标记表型符合率
Single coincidence rate (%)		 染色体
Chr.		 引物序列
Primer sequences (5°-3°)		 标记鉴定
Marker
identification		 标记联合使用表型符合率Comprehensive coincidence rate (%)
晚熟
Late maturity		 48 SCARA2-2 62.5 2 F: ACAGCTCGGCGAGAAAACAG
R: TCAAGCAATTAGGGCGGTG		 阳性
Positive		 87.5
SCARA4-21 58.3 4 F: TCACTTTGGCGACCACACTT
R: CAGACCCGCTTACGCTAAGAT		 阳性
Positive
SCARA5-16 60.4 5 F: TTTTTGTGATCAGGGGCGG
R: TGCATTGCATCCTCCCAAC		 阳性
Positive
早熟
Early maturity		 71 SCARA2-2 54.9 2 F: ACAGCTCGGCGAGAAAACAG
R: TCAAGCAATTAGGGCGGTG		 阴性
Negative		 93.0
SCARA4-21 66.2 4 F: TCACTTTGGCGACCACACTT
R: CAGACCCGCTTACGCTAAGAT		 阴性
Negative
SCARA5-16 76.1 5 F: TTTTTGTGATCAGGGGCGG’
R:TGCATTGCATCCTCCCAAC		 阴性
Negative
[1] 徐建飞, 金黎平. 马铃薯遗传育种研究: 现状与展望. 中国农业科学, 2017, 50: 990-1015.
Xu J F, Jin L P. Analysis for maturity of progenies from potato cultivar Zhongshu 3. Sci Agric Sin, 2017, 50: 990-1015. (in Chinese with English abstract)
[2] 孙慧生. 马铃薯育种学. 北京: 中国农业出版社, 2003. pp 30-59.
Sun H S. Potato Breeding. Beijing: China Agriculture Press, 2003. pp 30-59. (in Chinese)
[3] 徐建飞, 段绍光, 庞万福, 卞春松, 刘杰, 金黎平. 马铃薯品种中薯3号杂交后代熟性分析. 华北农学报, 2015, 30(增刊1): 92-96.
Xu J F, Duan S G, Pang W F, Bian C S, Liu J, Jin L P. Analysis for maturity of progenies from potato cultivar Zhongshu 3. Acta Agric Boreali-Sin, 2015, 30(S1): 92-96. (in Chinese with English abstract)
[4] Mackerron D K L, Davies H V. Markers for maturity and senescence in the potato crop. Potato Res, 1986, 29: 427-436.
doi: 10.1007/BF02357908
[5] Hvostova V V, Iacina I M. 马铃薯遗传学. 北京: 中国农业出版社, 1981. pp 280-283.
Hvostova V V, Iacina I M. Potato Genetics. Beijing: China Agriculture Press, 1981. pp 280-283. (in Chinese)
[6] Kloosterman B, Abelenda J A, Gomez M M C, Oortwijn M, De boer J M, Kowitwanich K, Horvath B M, Van Eck H J, Smaczniak C, Prat S, Visser R G F, Bachem C W B. Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature, 2013, 495: 246-250.
doi: 10.1038/nature11912
[7] Bonierbale M W, Plaisted R L, Tanksley S D. RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics, 1988, 120: 1095-1103.
doi: 10.1093/genetics/120.4.1095 pmid: 17246486
[8] Visker M H P W, Kerzer L C P, Van Eck H J, Jacobsen E, Colon L T, Struik P C. Can the QTL for late blight resistance on potato chromosome 5 be attributed to foliage maturity type? Theor Appl Genet, 2003, 106: 317-325.
pmid: 12582858
[9] Li X, Xu J, Duan S, Zhang J, Bian C, Hu J, Li G, Jin L. Mapping and QTL analysis of early-maturity traits in tetraploid potato (Solanum tuberosum L.). Int J Mol Sci, 2018, 19: 3065.
doi: 10.3390/ijms19103065
[10] Malosetti M, Visser R G F, Celis-Gamboa C, van Eeuwijk F A. QTL methodology for response curves on the basis of non-linear mixed models, with an illustration to senescence in potato. Theor Appl Genet, 2006, 113: 288-300.
pmid: 16791695
[11] Bradshaw J E, Hackett C A, Pande B, Waugh R, Bryan G J. QTL mapping of yield, agronomic and quality traits in tetraploid potato (Solanum tuberosum subsp. tuberosum). Theor Appl Genet, 2008, 116: 193-211.
doi: 10.1007/s00122-007-0659-1 pmid: 17938877
[12] Hackett C A, Bradshaw J E, Bryan G J. QTL mapping in autotetraploids using SNP dosage information. Theor Appl Genet, 2014, 127: 1885-1904.
doi: 10.1007/s00122-014-2347-2
[13] Massa A N, Manriquew-Carpintero N C, Coombs J J, Zarka D G, Boone A E, Wirk W W, Hackett C A, Bryan G J, Douches D S. Genetic linkage mapping of economically important traits in cultivated tetraploid potato (Solanum tuberosum L.). Genes Genom Genet, 2015, 5: 2357-2364.
[14] Massa A N, Manrique-Carpintero N C, Coombs J, Haynes K G, Bethke P C, Brandt T L, Gupta S K, Yencho G C, Novy R G, Douches D S. Linkage analysis and QTL mapping in a tetraploid russet mapping population of potato. BMC Genet, 2018, 19: 87.
doi: 10.1186/s12863-018-0672-1
[15] Jia L, Zhang B, Liu K, Zheng D, Wang X. Analysis of population genetic diversity of Cynoglossus cynoglossus based on 2b-RAD simplified genome sequencing. Fisher Res, 2017, 4: 125-133.
[16] Blanco-Bercial L, Buchlin A. New view of population genetics of zooplankton: RAD-seq analysis reveals population structure of the North Atlantic planktonic copepod Centropages typicus. Mol Ecol, 2016, 25: 1566-1580.
doi: 10.1111/mec.13581 pmid: 26857348
[17] Gao W, Qu J, Zhang J, Sonnenberg A, Chen Q, Zhang Y, Huang C. A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci. BMC Genomics, 2018, 19: 18.
doi: 10.1186/s12864-017-4421-z
[18] Seetharam A S, Stuart G W. Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments. PeerJ, 2013, 1: e226.
doi: 10.7717/peerj.226
[19] Dou J, Li X, Fu Q, Jiao W, Li Y, Li T, Wang Y, Hu X, Wang S, Bao Z. Evaluation of the 2b-RAD method for genomic selection in scallop breeding. Sci Rep, 2016, 6: 19244.
[20] 李兴翠, 李广存, 徐建飞, 段绍光, 卞春松, 庞万福, 刘杰, 金黎平. 四倍体马铃薯熟性连锁SCAR标记的开发与验证. 作物学报, 2017, 43: 821-828.
doi: 10.3724/SP.J.1006.2017.00821
Li X C, Li G C, Xu J F, Duan S G, Bian C S, Pang W F, Liu J, Jin L P. Development and verification of SCAR marker linked to maturity in tetraploid potato. Acta Agron Sin, 2017, 43: 821-828. (in Chinese with English abstract)
doi: 10.3724/SP.J.1006.2017.00821
[21] Oberhagemann P, Chatot-Balandras C, Schäfer-Pregl R, Wegener D, Palomino C, Salamini F, Bonnel E, GebhardT C. A genetic analysis of quantitative resistance to late blight in potato: towards marker-assisted selection. Mol Breed, 1999, 5: 399-415.
doi: 10.1023/A:1009623212180
[22] Collins A, Milbourne D, RamsaY L, Meyer R, Chatot-Balandras C, Oberhagemann P, De Jong W, Gebhardt C, Bonnel E, Waugh R. QTL for field resistance to late blight in potato are strongly correlated with maturity and vigour. Mol Breed, 1999, 5: 387-398.
doi: 10.1023/A:1009601427062
[23] Bradshaw J E, Pande B, Bryan G J, Hackett C A, McLean K, Stewart H E, Waugh R. Interval mapping of quantitative trait loci for resistance to late blight [Phytophthora infestans (Mont.) de Bary], height and maturity in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum). Genetics, 2004, 168: 983-995.
pmid: 15514069
[24] Visker M H P W, Heilersig H J B, Kodde L P, Van de Weg W E, Voorrips R E, Struik P C, Colon L T. Genetic linkage of QTLs for late blight resistance and foliage maturity type in six related potato progenies. Euphytica, 2005, 143: 189-199.
doi: 10.1007/s10681-005-3444-8
[25] Sliwka J, Jakuczun H, Lebecka R, Marczewski W, Gebhardt C, Zimnoch-Guzowska E. Tagging QTLs for late blight resistance and plant maturity from diploid wild relatives in a cultivated potato (Solanum tuberosum L.) background. Theor Appl Genet, 2007, 115: 101-112.
pmid: 17468842
[26] Li J, Wang Y, Wen G, Li G, Li Z, Zhang R, Ma S, Zhou J, Xie C. Mapping QTL underlying tuber starch content and plant maturity in tetraploid potato. Crop J, 2019, 7: 261-272.
doi: 10.1016/j.cj.2018.12.003
[27] 罗育, 黄春喜, 吴耀生, 蔡丹昭, 郭宏伟, 朱丹. 3种DNA分子标记法联合鉴别草珊瑚及其混伪品. 中草药, 2020, 51: 733-740.
Luo Y, Huang C X, Wu Y S, Cai D Z, Guo H W, Zhu D. Molecular authentication of Sarcandra glabra and its adulterants using three DNA molecular markers. Chin Trad Herbal Drugs, 2020, 51: 733-740. (in Chinese with English abstract)
[28] 黄艺宁. RAPD、ISSR分子标记联合鉴定毛木耳菌株的研究. 河南农业科学, 2020, 49(7): 118-125.
Huang Y N. RAPD and ISSR molecular identification of Auricularia cornea Ehrenb. J Henan Agric Sci, 2020, 49(7): 118-125. (in Chinese with English abstract)
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