Theoretical and Applied Genetics

, Volume 131, Issue 2, pp 267–282 | Cite as

Chromosomes A07 and A05 associated with stable and major QTLs for pod weight and size in cultivated peanut (Arachis hypogaea L.)

  • Huaiyong Luo
  • Jianbin Guo
  • Xiaoping Ren
  • Weigang Chen
  • Li Huang
  • Xiaojing Zhou
  • Yuning Chen
  • Nian Liu
  • Fei Xiong
  • Yong Lei
  • Boshou Liao
  • Huifang JiangEmail author
Original Article


Key message

Co-localized intervals and candidate genes were identified for major and stable QTLs controlling pod weight and size on chromosomes A07 and A05 in an RIL population across four environments.


Cultivated peanut (Arachis hypogaea L.) is an important legume crops grown in > 100 countries. Hundred-pod weight (HPW) is an important yield trait in peanut, but its underlying genetic mechanism was not well studied. In this study, a mapping population (Xuhua 13 × Zhonghua 6) with 187 recombinant inbred lines (RILs) was developed to map quantitative trait loci (QTLs) for HPW together with pod length (PL) and pod width (PW) by both unconditional and conditional QTL analyses. A genetic map covering 1756.48 cM was constructed with 817 markers. Additive effects, epistatic interactions, and genotype-by-environment interactions were analyzed using the phenotyping data generated across four environments. Twelve additive QTLs were identified on chromosomes A05, A07, and A08 by unconditional analysis, and five of them (qPLA07, qPLA05.1, qPWA07, qHPWA07.1, and qHPWA05.2) showed major and stable expressions in all environments. Conditional QTL mapping found that PL had stronger influences on HPW than PW. Notably, qHPWA07.1, qPLA07, and qPWA07 that explained 17.93–43.63% of the phenotypic variations of the three traits were co-localized in a 5 cM interval (1.48 Mb in physical map) on chromosome A07 with 147 candidate genes related to catalytic activity and metabolic process. In addition, qHPWA05.2 and qPLA05.1 were co-localized with minor QTL qPWA05.2 to a 1.3 cM genetic interval (280 kb in physical map) on chromosome A05 with 12 candidate genes. This study provides a comprehensive characterization of the genetic components controlling pod weight and size as well as candidate QTLs and genes for improving pod yield in future peanut breeding.



This study was supported by the National Natural Science Foundation of China (31271764, 31371662, 31471534, 31601340, and 31461143022), the China Agriculture Research System (CARS-14), and the National Plan for Science & Technology Support of China (2013BAD01B03). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standard

The experiments reported in the manuscript are in accordance with the ethical standards in China.

Supplementary material

122_2017_3000_MOESM1_ESM.jpg (290 kb)
Supplementary material 1 Figure S1 GO annotations of candidate genes in the co-localized interval on chromosome A07 (JPEG 290 kb)
122_2017_3000_MOESM2_ESM.jpg (179 kb)
Supplementary material 2 Figure S2 GO annotations of candidate genes in the co-localized interval on chromosome A05 (JPEG 178 kb)
122_2017_3000_MOESM3_ESM.docx (19 kb)
Supplementary material 3 Table S1 Descriptive statistics of phenotypic values of pod weight and size in the RIL population across four environments (DOCX 18 kb)
122_2017_3000_MOESM4_ESM.xlsx (147 kb)
Supplementary material 4 Table S2 Phenotyping data of the RIL population generated in four environments (XLSX 146 kb)
122_2017_3000_MOESM5_ESM.xlsx (55 kb)
Supplementary material 5 Table S3 Information of SSR markers genotyped in the RIL population (XLSX 54 kb)
122_2017_3000_MOESM6_ESM.xlsx (32 kb)
Supplementary material 6 Table S4 Genetic linkage map constructed based on 817 polymorphic loci in the RIL population (XLSX 31 kb)
122_2017_3000_MOESM7_ESM.xlsx (575 kb)
Supplementary material 7 Table S5 Genotyping data of the 817 mapped loci in the RIL population (XLSX 574 kb)
122_2017_3000_MOESM8_ESM.xlsx (79 kb)
Supplementary material 8 Table S6 Segregation of the genotypes of the 817 polymorphic loci in the RIL population (XLSX 79 kb)
122_2017_3000_MOESM9_ESM.xlsx (25 kb)
Supplementary material 9 Table S7 Functional annotations of candidate genes in the co-localized intervals on chromosomes A07 and A05 (XLSX 24 kb)
122_2017_3000_MOESM10_ESM.xlsx (10 kb)
Supplementary material 10 Table S8 KEGG pathways of candidate genes in the co-localized intervals on chromosomes A07 (XLSX 10 kb)


  1. Bednarek J, Boulaflous A, Girousse C, Ravel C, Tassy C, Barret P et al (2012) Down-regulation of the TaGW2 gene by RNA interference results in decreased grain size and weight in wheat. J Exp Bot 63:5945–5955CrossRefPubMedGoogle Scholar
  2. Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EK et al (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48:438–446CrossRefPubMedGoogle Scholar
  3. Bravo JP, Hoshino AA, Angelici CMLCD, Lopes CR, Gimenes MA (2006) Transferability and use of microsatellite markers for the genetic analysis of the germplasm of some Arachis section species of the genus Arachis. Genet Mol Biol 29:516–524CrossRefGoogle Scholar
  4. Chen W, Jiao Y, Cheng L, Huang L, Liao B, Tang M et al (2016) Quantitative trait locus analysis for pod- and kernel-related traits in the cultivated peanut (Arachis hypogaea L.). BMC Genet 17:25CrossRefPubMedPubMedCentralGoogle Scholar
  5. Chen Y, Ren X, Zheng Y, Zhou X, Huang L, Yan L et al (2017) Genetic mapping of yield traits using RIL population derived from Fuchuan Dahuasheng and ICG6375 of peanut (Arachis hypogaea L.). Mol Breed 37:17CrossRefPubMedPubMedCentralGoogle Scholar
  6. Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK (2008) Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol 8:1–11CrossRefGoogle Scholar
  7. Doyle J (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  8. FAOSTAT (2014) Production/Yield quantities of groundnuts, with shell in world + (Total). Food and agriculture organization of the united nations (FAO). Accessed 12 June 2017
  9. Faye I, Pandey MK, Hamidou F, Rathore A, Ndoye O, Vadez V, Varshney RK (2015) Identification of quantitative trait loci for yield and yield related traits in groundnut (Arachis hypogaea L.) under different water regimes in Niger and Senegal. Euphytica 206:631–647CrossRefPubMedPubMedCentralGoogle Scholar
  10. Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S (2004) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet 108:1064–1070CrossRefPubMedGoogle Scholar
  11. Fonceka D, Tossim HA, Rivallan R, Vignes H, Faye I, Ndoye O et al (2012) Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biol 12:26CrossRefPubMedPubMedCentralGoogle Scholar
  12. Gomes RLF, Lopes ÂCDA (2005) Correlations and path analysis in peanut. Crop Breed Appl Biot 5:105–112CrossRefGoogle Scholar
  13. Han YP, Teng WL, Wang Y, Zhao X, Wu L, Li DM, Li WB (2015) Unconditional and conditional QTL underlying the genetic interrelationships between soybean seed isoflavone, and protein or oil contents. Plant Breed 134:300–309CrossRefGoogle Scholar
  14. Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean RE, Kochert GD, Kresovich S (1999) Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Sci 39:1243–1247CrossRefGoogle Scholar
  15. Hu J, Wang Y, Fang Y, Zeng L, Xu J, Yu H et al (2015) A rare allele of GS2 enhances grain size and grain yield in rice. Mol Plant 8:1455–1465CrossRefPubMedGoogle Scholar
  16. Huang L, He HY, Chen WG, Ren XP, Chen YN, Zhou XJ et al (2015) Quantitative trait locus analysis of agronomic and quality-related traits in cultivated peanut (Arachis hypogaea L.). Theor Appl Genet 128:1103–1115CrossRefPubMedPubMedCentralGoogle Scholar
  17. Huang L, Wu B, Zhao J, Li H, Chen W, Zheng Y et al (2016) Characterization and transferable utility of microsatellite markers in the wild and cultivated Arachis species. PLoS ONE 11:e0156633CrossRefPubMedPubMedCentralGoogle Scholar
  18. Janila P, Variath MT, Pandey MK, Desmae H, Motagi BN, Okori P et al (2016) Genomic tools in groundnut breeding program: status and perspectives. Front Plant Sci 7:289CrossRefPubMedPubMedCentralGoogle Scholar
  19. Jiang H, Duan N, Ren X (2006) Descriptors and data standard for peanut (Arachis spp.). China Agriculture Press, BeijingGoogle Scholar
  20. Johnson CS, Kolevski B, Smyth DR (2002) TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. Plant Cell 14:1359–1375CrossRefPubMedPubMedCentralGoogle Scholar
  21. Kang X, Li W, Zhou Y, Ni M (2013) A WRKY transcription factor recruits the SYG1-like protein SHB1 to activate gene expression and seed cavity enlargement. PLoS Genet 9:e1003347CrossRefPubMedPubMedCentralGoogle Scholar
  22. Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H, Sakai H et al (2012) Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. Mol Breed 30:125–138CrossRefPubMedGoogle Scholar
  23. Kosambi DD (1943) The estimation of map distances from recombination values. Ann Hum Genet 12:172–175Google Scholar
  24. Leal-Bertioli SC, Jose AC, Alves-Freitas DM, Moretzsohn MC, Guimaraes PM, Nielen S et al (2009) Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biol 9:112CrossRefPubMedPubMedCentralGoogle Scholar
  25. Li N, Li Y (2016) Signaling pathways of seed size control in plants. Curr Opin Plant Biol 33:23–32CrossRefPubMedGoogle Scholar
  26. Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L et al (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269CrossRefPubMedGoogle Scholar
  27. Li JC, Lindqvist-Kreuze H, Tian ZD, Liu J, Song BT, Landeo J et al (2012a) Conditional QTL underlying resistance to late blight in a diploid potato population. Theor Appl Genet 124:1339–1350CrossRefPubMedGoogle Scholar
  28. Li S, Liu Y, Zheng L, Chen L, Li N, Corke F et al (2012b) The plant-specific G protein gamma subunit AGG3 influences organ size and shape in Arabidopsis thaliana. New Phytol 194:690–703CrossRefPubMedGoogle Scholar
  29. Li QF, Zhang Y, Liu TT, Wang FF, Liu K, Chen JS, Tian JC (2015) Genetic analysis of kernel weight and kernel size in wheat (Triticum aestivum L.) using unconditional and conditional QTL mapping. Mol Breed 35:194CrossRefGoogle Scholar
  30. Liang X, Chen X, Hong Y, Liu H, Zhou G, Li S, Guo B (2009) Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. BMC Plant Biol 9:35CrossRefPubMedPubMedCentralGoogle Scholar
  31. Liu GF, Zhu HT, Liu SW, Zeng RZ, Zhang ZM, Li WT et al (2010) Unconditional and conditional QTL mapping for the developmental behavior of tiller number in rice (Oryza sativa L.). Genetica 138:885–893CrossRefPubMedGoogle Scholar
  32. Luo H, Ren X, Li Z, Xu Z, Li X, Huang L et al (2017a) Co-localization of major quantitative trait loci for pod size and weight to a 3.7 cM interval on chromosome A05 in cultivated peanut (Arachis hypogaea L.). BMC Genom 18:58CrossRefGoogle Scholar
  33. Luo H, Xu Z, Li Z, Li X, Lv J, Ren X et al (2017b) Development of SSR markers and identification of major quantitative trait loci controlling shelling percentage in cultivated peanut (Arachis hypogaea L.). Theor Appl Genet. doi: 10.1007/s00122-017-2915-3 Google Scholar
  34. Macedo SE, Moretzsohn MC, Leal-Bertioli SC, Alves DM, Gouvea EG, Azevedo VC, Bertioli DJ (2012) Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut. BMC Res Notes 5:86CrossRefPubMedPubMedCentralGoogle Scholar
  35. Mao H, Sun S, Yao J, Wang C, Yu S, Xu C et al (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107:19579–19584CrossRefPubMedPubMedCentralGoogle Scholar
  36. Moretzsohn Mde C, Hopkins MS, Mitchell SE, Kresovich S, Valls JF, Ferreira ME (2004) Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome. BMC Plant Biol 4:11CrossRefPubMedGoogle Scholar
  37. Moretzsohn MC, Leoi L, Proite K, Guimaraes PM, Leal-Bertioli SC, Gimenes MA et al (2005) A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111:1060–1071CrossRefPubMedGoogle Scholar
  38. Moretzsohn MC, Barbosa AV, Alves-Freitas DM, Teixeira C, Leal-Bertioli SC, Guimaraes PM et al (2009) A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol 9:40CrossRefPubMedPubMedCentralGoogle Scholar
  39. Nagy ED, Chu Y, Guo Y, Khanal S, Tang S, Li Y et al (2010) Recombination is suppressed in an alien introgression in peanut harboring Rma, a dominant root-knot nematode resistance gene. Mol Breed 26:357–370CrossRefGoogle Scholar
  40. Naito Y, Suzuki S, Iwata Y, Kuboyama T (2008) Genetic diversity and relationship analysis of peanut germplasm using SSR markers. Breed Sci 58:293–300CrossRefGoogle Scholar
  41. Proite K, Leal-Bertioli SCM, Bertioli DJ, Moretzsohn MC, da Silva FR, Martins NF, Guimaraes PM (2007) ESTs from a wild Arachis species for gene discovery and marker development. BMC Plant Biol 7:7CrossRefPubMedPubMedCentralGoogle Scholar
  42. Qin H, Feng S, Chen C, Guo Y, Knapp S, Culbreath A et al (2012) An integrated genetic linkage map of cultivated peanut (Arachis hypogaea L.) constructed from two RIL populations. Theor Appl Genet 124:653–664CrossRefPubMedGoogle Scholar
  43. Ravi K, Vadez V, Isobe S, Mir RR, Guo Y, Nigam SN et al (2011) Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.). Theor Appl Genet 122:1119–1132CrossRefPubMedGoogle Scholar
  44. Schruff MC, Spielman M, Tiwari S, Adams S, Fenby N, Scott RJ (2006) The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development 133:251–261CrossRefPubMedGoogle Scholar
  45. Selvaraj MG, Narayana M, Schubert AM, Ayers JL, Baring MR, Burow MD (2009) Identification of QTLs for pod and kernel traits in cultivated peanut by bulked segregant analysis. Electron J Biotechnol 12:1–10Google Scholar
  46. Sharma KK, Bhatnagar-Mathur P (2006) Peanut (Arachis hypogaea L.). Methods Mol Biol 343:347–358PubMedGoogle Scholar
  47. Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M et al (2012) In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol 12:80CrossRefPubMedPubMedCentralGoogle Scholar
  48. Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SC, Thudi M et al (2013) Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 20:173–184CrossRefPubMedPubMedCentralGoogle Scholar
  49. Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630CrossRefPubMedGoogle Scholar
  50. Sukruth M, Paratwagh SA, Sujay V, Kumari V, Gowda MVC, Nadaf HL et al (2015) Validation of markers linked to late leaf spot and rust resistance, and selection of superior genotypes among diverse recombinant inbred lines and backcross lines in peanut (Arachis hypogaea L.). Euphytica 204:343–351CrossRefGoogle Scholar
  51. Van Ooijen JW (2006) JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Wageningen, KyazmaGoogle Scholar
  52. Varshney RK, Pandey MK, Janila P, Nigam SN, Sudini H, Gowda MV et al (2014) Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theor Appl Genet 127:1771–1781CrossRefPubMedPubMedCentralGoogle Scholar
  53. Varshney RK, Saxena RK, Upadhyaya HD, Khan AW, Yu Y, Kim C et al (2017) Whole-genome resequencing of 292 pigeon pea accessions identifies genomic regions associated with domestication and agronomic traits. Nat Genet. doi: 10.1038/ng.3872 PubMedGoogle Scholar
  54. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78CrossRefPubMedGoogle Scholar
  55. Wang H, Penmetsa RV, Yuan M, Gong L, Zhao Y, Guo B et al (2012) Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.). BMC Plant Biol 12:1–11CrossRefGoogle Scholar
  56. Wen YX, Zhu J (2005) Multivariable conditional analysis for complex trait and its components. Acta Genet Sin 32:289–296PubMedGoogle Scholar
  57. Xia T, Li N, Dumenil J, Li J, Kamenski A, Bevan MW et al (2013) The ubiquitin receptor DA1 interacts with the E3 ubiquitin ligase DA2 to regulate seed and organ size in Arabidopsis. Plant Cell 25:3347–3359CrossRefPubMedPubMedCentralGoogle Scholar
  58. Xing Z, Tan F, Hua P, Sun L, Xu G, Zhang Q (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105:248–257CrossRefPubMedGoogle Scholar
  59. Yang J, Zhu J, Williams RW (2007) Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics 23:1527–1536CrossRefPubMedGoogle Scholar
  60. Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J (2008) QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics 24:721–723CrossRefPubMedGoogle Scholar
  61. Zhang J, Liang S, Duan J, Wang J, Chen S, Cheng Z et al (2012) De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.). BMC Genom 13:90CrossRefGoogle Scholar
  62. Zhang ZH, Wu XY, Shi CN, Wang RN, Li SF, Wang ZH et al (2016) Genetic dissection of the maize kernel development process via conditional QTL mapping for three developing kernel-related traits in an immortalized F2 population. Mol Genet Genom 291:437–454CrossRefGoogle Scholar
  63. Zhou X, Dong Y, Zhao J, Huang L, Ren X, Chen Y et al (2016a) Genomic survey sequencing for development and validation of single-locus SSR markers in peanut (Arachis hypogaea L.). BMC Genom 17:420CrossRefGoogle Scholar
  64. Zhou X, Xia Y, Liao J, Liu K, Li Q, Dong Y et al (2016b) Quantitative trait locus analysis of late leaf spot resistance and plant-type-related traits in cultivated peanut (Arachis hypogaea L.) under multi-environments. PLoS ONE 11:e0166873CrossRefPubMedPubMedCentralGoogle Scholar
  65. Zhu J (1995) Analysis of conditional genetic-effects and variance-components in developmental genetics. Genetics 141:1633–1639PubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Huaiyong Luo
    • 1
  • Jianbin Guo
    • 1
  • Xiaoping Ren
    • 1
  • Weigang Chen
    • 1
  • Li Huang
    • 1
  • Xiaojing Zhou
    • 1
  • Yuning Chen
    • 1
  • Nian Liu
    • 1
  • Fei Xiong
    • 2
  • Yong Lei
    • 1
  • Boshou Liao
    • 1
  • Huifang Jiang
    • 1
    Email author
  1. 1.Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural SciencesWuhanChina
  2. 2.Huanggang Academy of Agricultural SciencesHuanggangChina

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