Skip to main content
SpringerLink
Log in

Development of SCAR markers linked to sin-2, the stringless pod trait in pea (Pisum sativum L.)

Molecular Breeding Aims and scope Submit manuscript

Cite this article

Abstract

With increasing consumer demand for vegetables, edible-podded peas have become more popular. Stringlessness is one of most important traits for snap peas. A single recessive gene, sin-2, controls this trait. Because pollen carrying the stringless gene is less competitive than pollen carrying the stringy gene, there are fewer than expected stringless plants recovered in segregating generations. Marker-assisted selection (MAS) is a valuable tool to identify plants with the traits of interest at an early stage in the breeding process. The objective of this study was to identify robust, user-friendly molecular markers tightly linked to sin-2. A total of 144 target region amplification polymorphism (TRAP) primer combinations were used to screen four DNA bulks, which were constructed from 32 pea breeding lines based on their phenotypes. Sixty polymorphic TRAP primer combinations were identified between bulks of stringless and stringy pods. Five primer combinations, F6_Trap03_168, F6_SA12_145, F10_ODD8_130, F11_GA5_850, and F12_SA12_190, showed more than 90 % association with the stringless phenotype in 32 pea breeding lines. Two of the TRAP markers, F10_ODD8_130 and F12_SA12_190, were cloned, sequenced, and successfully converted to sequence characterized amplified region (SCAR) markers. These two SCAR markers were validated using 20 F5 recombinant inbred lines derived from a cross between Bohatyr (a dry pea variety with strings) and S1188 (a stringless snap pea variety) and showed strong marker-trait association. The results will have direct application in MAS of stringless edible-podded peas.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

References

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25(17):3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bastianelli D, Grosjean F, Peyronnet C, Duparque M, Regnier J (1998) Feeding value of pea (Pisum sativum, L.). 1. Chemical composition of different categories of pea. Anim Sci 67(3):609–620

    Article  Google Scholar 

  • Chen J, Hu J, Vick BA, Jan C (2006) Molecular mapping of a nuclear male-sterility gene in sunflower (Helianthus annuus L.) using TRAP and SSR markers. Theor Appl Genet 113(1):122–127

    Article  CAS  PubMed  Google Scholar 

  • Currence TM (1930) Inheritance studies in Phaseolus vulgaris. Tech Bull Minn Agric Exp Stn 68:1–28

  • Don R, Cox P, Wainwright B, Baker K, Mattick J (1991) ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucl Acids Res 19(14):4008

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gioia T, Logozzo G, Kami J, Zeuli PS, Gepts P (2013) Identification and characterization of a homologue to the Arabidopsis INDEHISCENT gene in common bean. J Hered 104(2):273–286

    Article  CAS  PubMed  Google Scholar 

  • Goodwin SB, Cavaletto JR, Hale IL, Thompson I, Xu SS, Adhikari TB, Dubcovsky J (2015) A new map location of gene Stb3 for resistance to Septoria tritici blotch in wheat. Crop Sci 55(1):35–43. doi:10.2135/cropsci2013.11.0766

    Article  CAS  Google Scholar 

  • Gritton ET, Hagedorn DJ (1975) Linkage of the genes SBM and WLO in peas. Crop Sci 15(3):447–448. doi:10.2135/cropsci1975.0011183X001500030051x

    Article  Google Scholar 

  • Hao H, Chen T, Fan L, Li R, Wang X (2013) 2, 6-Dichlorobenzonitrile causes multiple effects on pollen tube growth beyond altering cellulose synthesis in Pinus bungeana Zucc. PLoS ONE 8(10):e76660. doi:10.1371/journal.pone.0076660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu J, Vick B (2003) Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Mol Biol Rep 21(3):289–294. doi:10.1007/BF02772804

    Article  CAS  Google Scholar 

  • Hu J, Seiler GJ, Jan C-C, Vick BA (2003) Assessing genetic variability among sixteen perennial Helianthus species using PCR-based TRAP markers. In: Proceedings of 25th sunflower research forum. http://www.sunflowernsa.com/research/research-workshop/documents/88.PDF. Accessed 21 Nov 2005

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9(9):868–877

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kang S-T, Kwak M, Kim H-K, Choung M-G, Han W-Y, Baek I-Y, Kim MY, Van K, Lee S-H (2009) Population-specific QTLs and their different epistatic interactions for pod dehiscence in soybean [Glycine max (L.) Merr.]. Euphytica 166(1):15–24

    Article  Google Scholar 

  • Koinange EM, Singh SP, Gepts P (1996) Genetic control of the domestication syndrome in common bean. Crop Sci 36(4):1037–1045

    Article  Google Scholar 

  • Kwon SJ, Smykal P, Hu J, Wang M, Kim S-J, McGee RJ, McPhee K, Coyne CJ (2013) User-friendly markers linked to fusarium wilt race 1 resistance Fw gene for marker-assisted selection in pea. Plant Breeding 132(6):642–648

    Article  CAS  Google Scholar 

  • Lamprecht H (1938) Über Hülseneigenschaften bei Pisum, ihre Vererbung und ihr züchterischer Wert. Theor Appl Genet 10(6):150–157

    Article  Google Scholar 

  • Lamprecht H, Mrkos H (1950) Die vererbung des vorblattes bei Pisum sowie die koppelung des gens Br. Agri Hort Genet 8:153–162

    Google Scholar 

  • Lazzaro MD, Donohue JM, Soodavar FM (2003) Disruption of cellulose synthesis by isoxaben causes tip swelling and disorganizes cortical microtubules in elongating conifer pollen tubes. Protoplasma 220(3–4):201–207. doi:10.1007/s00709-002-0042-7

    Article  CAS  PubMed  Google Scholar 

  • Macas J, Neumann P, Navrátilová A (2007) Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genom 8(1):427

    Article  Google Scholar 

  • Main D, Cheng C-H, Ficklin SP, Sanad M, Jung S, Lee T, Zheng P, Coyne C, McGee R, Mockaitis K (2014) The cool season food legume database: an integrated resource for basic, translational and applied research. In Plant and Animal Genome XXII Conference.  Plant and Animal Genome. San Diego, USA

  • McGee RJ, Baggett JR (1992a) Inheritance of stringless pod in Pisum sativum L. J Am Soc Hortic Sci 117(4):628–632

    Google Scholar 

  • McGee RJ, Baggett JR (1992b) Unequal growth rate of pollen tubes from normal and stringless pea genotypes. HortScience 27(7):833–834

    Google Scholar 

  • Menzo V, Giancaspro A, Giove S, Nigro D, Zacheo S, Colasuonno P, Marcotuli I, Incerti O, Blanco A, Gadaleta A (2013) TRAP molecular markers as a system for saturation of the genetic map of durum wheat. Euphytica 194(2):151–160. doi:10.1007/s10681-013-0891-5

    Article  CAS  Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. PNAS 88(21):9828–9832. doi:10.1073/pnas.88.21.9828

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miklas PN, Hu J, Grünwald NJ, Larsen KM (2006) Potential application of TRAP (targeted region amplified polymorphism) markers for mapping and tagging disease resistance traits in common bean. Crop Sci 46(2):910–916

    Article  CAS  Google Scholar 

  • Myers JR, Baggett JR, Lamborn C (2001) Origin, history, and genetic improvement of the snap pea (Pisum sativum L.). Plant Breed Rev 21:93

    CAS  Google Scholar 

  • Novák P, Neumann P, Macas J (2010) Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data. BMC Bioinform 11(1):378

    Article  Google Scholar 

  • Rojas-Barros P, Hu J, Jan C (2008) Molecular mapping of an apical branching gene of cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 117(1):19–28

    Article  CAS  PubMed  Google Scholar 

  • Shelmidine JJ, Hartmann RW (1984) Evidence for two recessive genes and two dominant genes controlling string development in one bean population. Annu Rep Bean Improv Coop 27:117–119

    Google Scholar 

  • Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA (2007) Primer3Plus, an enhanced web interface to Primer3. Nucl Acids Res 35(suppl 2):W71–W74

    Article  PubMed  PubMed Central  Google Scholar 

  • Weeden NF (2007) Genetic changes accompanying the domestication of Pisum sativum: is there a common genetic basis to the ‘domestication syndrome’ for legumes? Ann Bot 100(5):1017–1025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wehner T, Gritton E (1981) Effect of the n gene on pea pod characteristics. J Am Soc Hortic Sci 106:181–183

  • Wellensiek S (1971) Lamprecht’s gene sin for stringless. Pisum Newsl 3:48

    Google Scholar 

  • White OE (1917) Studies of inheritance in Pisum. II. The present state of knowledge of heredity and variation in peas. Proc Am Philos Soc 56(7):487–588

    Google Scholar 

  • Williams JG, Reiter RS, Young RM, Scolnik PA (1993) Genetic mapping of mutations using phenotypic pools and mapped RAPD markers. Nucl Acids Res 21(11):2697–2702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yue B, Vick BA, Cai X, Hu J (2010) Genetic mapping for the Rf1 (fertility restoration) gene in sunflower (Helianthus annuus L.) by SSR and TRAP markers. Plant Breed 129(1):24–28. doi:10.1111/j.1439-0523.2009.01661.x

    Article  CAS  Google Scholar 

  • Zaumeyer W (1963) Some new Tendercrop mutants. Seed World March 8:8–10

    Google Scholar 

Download references

Acknowledgments

The authors gratefully acknowledge the funding sources: USDA-ARS CRIS Projects #2090-21000-028-00D (JH, CJC) and 2090-21000-024-00D (RJM). Liangsheng Xu and Lisa Taylor are greatly acknowledged for their technical assistance. Also, thanks for the support from Washington State University.

Author information

Authors and Affiliations

  1. Department of Horticulture, Washington State University, Pullman, WA, 99164, USA

    Yu Ma, Dorrie Main & Jodi Humann

  2. Plant Germplasm Introduction and Testing, USDA ARS, Pullman, WA, 99164, USA

    Jinguo Hu & Clarice J. Coyne

  3. Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA

    James R. Myers

  4. Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14850, USA

    Michael Mazourek

  5. Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA

    Meinan Wang

  6. Grain Legume Genetics and Physiology Research Unit, USDA ARS, Pullman, WA, 99164, USA

    Rebecca J. McGee

Authors
  1. Yu Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jinguo Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. James R. Myers
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michael Mazourek
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Clarice J. Coyne
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dorrie Main
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Meinan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jodi Humann
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Rebecca J. McGee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rebecca J. McGee.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource 1

Characteristics of 32 pea breeding lines and corresponding genotypes of the five TRAP markers (F6_Trap03_168, F6_SA12_145, F10_ODD8_130, F11_GA5_850 and F12_SA12_190) and the two SCAR markers (SC_F10_ODD8_130 and SC_F12_SA12_190) (DOCX 15 kb)

Online Resource 2

Characteristics of 20 RIL individuals and corresponding genotypes of the five TRAP markers (F6_Trap03_168, F6_SA12_145, F10_ODD8_130, F11_GA5_850 and F12_SA12_190) and the two SCAR markers (SC_F10_ODD8_130 and SC_F12_SA12_190) (DOCX 13 kb)

Online Resource 2

A The string is absent in pod sutures of stringless pea individual. B There is no string in the ventral suture when breaking it apart by hand. C The strings are present in pod sutures of stringy pea individuals. D There are strings in the ventral sutures when breaking them apart by hand. (PPTX 1004 kb)

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ma, Y., Hu, J., Myers, J.R. et al. Development of SCAR markers linked to sin-2, the stringless pod trait in pea (Pisum sativum L.). Mol Breeding 36, 105 (2016). https://doi.org/10.1007/s11032-016-0525-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-016-0525-4

Keywords

search

Navigation