Czech J. Genet. Plant Breed., 2023, 59(2):95-108 | DOI: 10.17221/74/2022-CJGPB

QTL localisation of seed-related traits in Tibetan hulless barley based on a high-density single-nucleotide polymorphism genetic mapOriginal Paper

Yan Wang1,2, Xiaohua Yao1,2*, Youhua Yao1,2, Yixiong Bai1,2, Likun An1,2, Xin Li1,2, Yongmei Cui1,2, Kunlun Wu1,2*
1 Qinghai University, Xining, P.R. China
2 Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai Subcenter of National Hulless Barley Improvement, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Qinghai Academy of Agricultural and Forestry Sciences, Xining, P.R. China

The effective use of high-quality and high-yielding germplasm resources is of great importance for the development of hulless barley varieties. Therefore, the search for such resources has long been a goal of the breeding community. In this study, a genotyping-by-sequencing (GBS) analysis was performed on an F2 (Nierumuzha × Kunlun 10) population. A high-density genetic map of hulless barley was constructed, which contained 1 475 efficient single-nucleotide polymorphism markers with 7 052 bin markers. The total length of the seven chromosomes was 1 139.4 cM, with an average marker distance of 0.59 cM. Based on this high-density linkage map, a total of 54 quantitative trait loci (QTLs) related to the seed traits were detected, including seed colour (SC), thousand kernel weight (TKW), seed average area (SAA), seed perimeter (SP), seed length (SL), seed width (SW), seed length/width (SLW), seed diameter (SD), and seed circular degree (SCD). These QTLs explained 3.32–35.73% (mean = 11.45%) of the phenotypic interpretation, including 24 main QTLs and 30 epistatic QTLs. A total of 24 candidate genes were identified within the QTL region, including one SC-associated transcription factor (ANT1), two TSW-related genes, a transcription factor (NAC021), a gene associated with the non-homologous end joining (NHEJ) pathway (ku70), three SAA-associated genes (LOL2, NAC021, TSK), two SL-associated genes (MADS21, MADS4), six SW-associated genes (FIP1, NAC021, DREB 1A, HVA22A, CYP78A6, SAUR71), five LW-related genes (NAM-B2, CRY1, LHY, CYP710A1, WRKY72), two SP-related genes (SKIP11, TCP18), two SD-related genes (NAC021, SKIP8), and three SCD-related genes (MYB1R1, RAX3, NAC100). These genes are involved in the regulation of the cell development, material transport, signal transduction, and plant morphogenesis and play an important role in the regulation of agronomic traits in hulless barley. The high-density genetic mapping and QTL identification of the seed traits in hulless barley provide a valuable genetic resource and the basis for further molecular marker-assisted selection and genomic studies.

Keywords: genotyping-by-sequencing (GBS); linkage analysis; quantitative trait loci; seed traits

Received: August 7, 2022; Accepted: November 10, 2022; Prepublished online: January 31, 2023; Published: March 13, 2023  Show citation

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Wang Y, Yao X, Yao Y, Bai Y, An L, Li X, et al.. QTL localisation of seed-related traits in Tibetan hulless barley based on a high-density single-nucleotide polymorphism genetic map. Czech J. Genet. Plant Breed. 2023;59(2):95-108. doi: 10.17221/74/2022-CJGPB.
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    References

    1. Aaron M., Matthew H., Eric B. (2010): The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20: 1297-1303. Go to original source... Go to PubMed...
    2. Bellido G.G., Beta T. (2009): Anthocyanin composition and oxygen radical scavenging capacity (ORAC) of milled and pearled purple, black, and common barley. Journal of Agricultural and Food Chemistry, 57: 1022-1028. Go to original source... Go to PubMed...
    3. Canamero R.C., Bakrim N., Bouly J.P. (2006): Cryptochrome photoreceptors cry1 and cry2 antagonistically regulate primary root elongation in Arabidopsis thaliana. Planta, 224: 995-1003. Go to original source... Go to PubMed...
    4. Chen Z.L., Wang B.B., Dong X.M., Liu H., Ren L.H., Chen J., Andrew. (2014): An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population. BMC Genomics, 15: 433. Go to original source... Go to PubMed...
    5. Cui Z., Tong A., Huo Y. (2017): SKIP controls flowering time via the alternative splicing of SEF pre-mRNA in Arabidopsis. BMC Bioinformatics, 15: 80. Go to original source... Go to PubMed...
    6. Fell V.L., Schild-Poulter C. (2015): The Ku heterodimer: Function in DNA repair and beyond. Mutation Research, 763: 15-29. Go to original source... Go to PubMed...
    7. Han J.Q., Hong Q.Y. (2020): Research progress of bioactive ingredients and physiological functions in hulless barley. Journal of Food Science and Technology, 38: 11-20.
    8. He L.H., Zhao S.J., Hu Z.B. (2008): Advances in plant cytochrome P450 genes and functions. Drug Biotechnology, 15: 142-147.
    9. He M.Z., Huang J., Du L.E., Wen Q.S., Chen J., Tian M.L. (2019): Progress in the study of TONSOKU gene in Arabidopsis thaliana. Molecular Plant Breeding, 17: 1175-1185.
    10. Hussain W., Baenziger P.S., Belamkar V. (2017): Genotyping-by-sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Scientific Reports, 7: 16394. Go to original source... Go to PubMed...
    11. Lai X., Vega-Léon R., Hugouvieux V. (2021): The intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors. Nature Communications, 12: 4760. Go to original source... Go to PubMed...
    12. Li H., Durbin R. (2009): Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25: 1754-1760. Go to original source... Go to PubMed...
    13. Li X., Yu X.L., Yao X.H., Yao Y.H., Bai Y.X., An L.K., Wu K.L. (2021): Mapping the major quantitative trait loci of the heading date trait in Qingke barley (Hordeum vulgare L.) from the Qinghai-Tibetan Plateau via genotyping by sequencing. All Life, 14: 882-893. Go to original source...
    14. Liang X., Gao M., Sikandar Amanullah., Yu G., Xiu J.L., Hong G.X., Ji X.L., Yue G., Cheng Z.Y., Fei S.L. (2022): Identification of QTLs linked with watermelon fruit and seed traits using GBS-based high-resolution genetic mapping, Scientia Horticulturae, 303: 111237. Go to original source...
    15. Liu N., Li M., Hu X. (2017): Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing. BMC Genomics, 18: 466. Go to original source... Go to PubMed...
    16. Nie C., Yan X., Xie X., Zhang Z., Zhu J., Wang Y., Li J. (2021): Structure of β-glucan from Tibetan hull-less barley and its in vitro fermentation by human gut microbiota. Chemical and Biological Technologies in Agriculture, 8: 1-14. Go to original source...
    17. Qiao Y., Sun J.Q., Wei R.Q., Liu Y. (2019): Research progress of GBS technology in plants. China Agricultural Science and Technology Herald, 21: 47-55.
    18. Qiu T., Chen Y., Li M. (2013): The tissue-specific and developmentally regulated expression patterns of the SAUR41 subfamily of SMALL AUXIN UP RNA genes: Potential implications. Plant Signaling & Behavior, 8: e25283. Go to original source... Go to PubMed...
    19. Schafleitner R., Huang S.M., Chu S.H., Yen J.Y., Lin C.Y., Yan M.R., Krishnan B., Liu M.S., Lo H.F., Chen C.Y., Chen L.F, Wu D.C., Bui T.G., Ramasamy S., Tung C.W., Nair R. (2016): Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis. BMC Plant Biology, 16: 159. Go to original source... Go to PubMed...
    20. Shahnejat-Bushehri S., Tarkowska D., Sakuraba Y. (2016): Arabidopsis NAC transcription factor JUB1 regulates GA/BR metabolism and signalling. Nature Plants, 2: 16013. Go to original source... Go to PubMed...
    21. Shan R.Y., Chen C.S., Zhong Q.S., Lin Z.H., Chen Z.H., You X.M. (2018): Cloning and differential expression characterization of CYP710A1, a cytochrome P450 gene from tea tree. Journal of Tea, 59: 181-185.
    22. Song B.W., Dang X.X., Zhao Z., Chen C., Huang M., Chen W.X., Liang K.Q., Xiao W.M. (2022): Localization and analysis of grain shape QTL in rice based on high-density genetic mapping. Journal of Crop Science, 48: 1-17.
    23. Van Ooijen J.W. (2009): MapQTL 6.0.: Software for the Mapping of Quantitative Trait Loci in Experimental Populations of Diploid Species. Wageningen, Kyazma.
    24. Wang J.C. (2021): Progress in the study of TCP family genes in plants. Agriculture and Technology, 41: 63-66. Go to original source...
    25. Wang J., Zheng C., Shao X. (2020a): Transcriptomic and genetic approaches reveal an essential role of the NAC transcription factor SlNAP1 in the growth and defense response of tomato. Horticulture Research, 7: 209. Go to original source... Go to PubMed...
    26. Wang J., Wang Y., Zhang J. (2021): The NAC transcription factor ClNAC68 positively regulates sugar content and seed development in watermelon by repressing ClINV and ClGH3.6. Horticulture Research, 8: 214. Go to original source... Go to PubMed...
    27. Wang N., Yuan Y., Wang H. (2020b): Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding. Scientific Reports, 10: 16308. Go to original source... Go to PubMed...
    28. Wang X., Li Z., Yan F. (2013): ZmSKIP, a homologue of SKIP in maize, is involved in response to abiotic stress in tobacco. Plant Cell, Tissue and Organ Culture, 112: 203-216. Go to original source...
    29. Wang X.Q., Chen B.J., Yin L.P. (2003): MYB transcription factors in plants. Biotechnology Bulletin, 2: 22-25.
    30. Wang X.R., Li Y., Zhang Y.J., Li Y.S., Wang J.C., Xu Y.P., Qi X.S. (2022): Identification of drought resistance of barley germplasm resources at the establishment stage and screening of drought tolerance indicators. Journal of Crop Science, 48: 1279-1287. Go to original source...
    31. Xue X.J., Du X.Y., Gai Y., Tang Y., Sun Y.X., Song L.Q., Jiang Z.W. (2020): Progress of developing SNPs in plants based on GBS sequencing. Jiangsu Agricultural Science, 48: 62-68.
    32. Yang D.S., Yu Z., Yu X.X., Li J.Q., Li J.W., Wu G.F., Lu Q.Q. (2021): Construction of an ultra-high density genetic linkage map of tetraploid hybrid ice grass based on GBS technology. Journal of Cereal Crops, 41: 1197-1210.
    33. Yao X.H., Wu K.L., Yao Y.H. (2018): Construction of a high-density genetic map: Genotyping by sequencing (GBS) to map purple seed coat color (Psc) in hulless barley. Hereditas, 155: 37. Go to original source... Go to PubMed...
    34. Yao H., Wang Y., Yin J., Nie S., Xie, M. (2021): Isolation, physicochemical properties, and structural characteristics of arabinoxylan from hull-less barley. Molecules, 26: 3026. Go to original source... Go to PubMed...
    35. Yao X.H., Wang Y., Yao Y.H., An L.K., Wang Y., Wu K.L. (2022): Cloning and expression of a new gene HvMEL1 AGO in hulless barley under stripe disease stress. Journal of Crop Science, 48: 1181-1190. Go to original source...
    36. Zhang L., Zhang B.J. (2017): Localization and cloning of genes for quantitative traits in plants. Botany Bulletin, 24: 553-560.

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