Gene Mapping of Sorghum Flowering Time and Prediction of Candidate Genes Based on BSA-seq

doi:10.13560/j.cnki.biotech.bull.1985.2025-0890

Abstract

Abstract:

Objective Flowering time is a key target trait in sorghum breeding, significantly influencing its ecological adaptability and high-yield potential. Method An F₂ population derived from a cross between the late-flowering variety Hongyingzi and the early-flowering variety SAP001 was used for genetic mapping of flowering time. Result Phenotypic investigation revealed that the segregation ratio of late-flowering and early-flowering plants was consistent with 3∶1(χ²=0.225, P>0.05), indicating that the trait was controlled by a pair of major genes. BSA-Seq analysis of extreme early-and late-flowering lines detected a genetic locus significantly associated with flowering time within the 59.73‒60.44 Mb interval on chromosome 3. By integrating whole-genome resequencing of the parents and transcriptome data, a key candidate gene (SbiHYZ.03G218800), encoding a light-harvesting complex Ⅱ chlorophyll-binding protein, was identified as a putative novel regulator of flowering time in sorghum (Sorghum bicolor (L.)Moench). There were mutations in the binding sites of Myb/SANT and TATA-binding protein (TBP) within its promoter region, and the expression of this gene differed significantly between the parents, possibly it was a new gene regulating flowering time of sorghum. Based on SNP and InDel variations in this candidate region, a closely linked molecular marker effectively distinguishing between early- and late-flowering plants was developed. Conclusion This study preliminarily reveals the genetic basis of flowering time in Chinese liquor-brewing sorghum germplasm and provides valuable genetic resources and molecular markers for molecular breeding of sorghum maturity.

Key words: sorghum, flowering time, BSA-seq, transcriptome sequencing, candidate genes

WANG Shang-feng, CHENG Bin, WANG Ruo-ruo, DING Yan-qing, XU Jian-xia, CAO Ning, GAO Xu, LI Wen-zhen, ZHANG Li-yi. Gene Mapping of Sorghum Flowering Time and Prediction of Candidate Genes Based on BSA-seq[J]. Biotechnology Bulletin, 2026, 42(2): 197-206.

Figures/Tables 9

References 51

[1]	王艳秋, 张飞, 朱凯, 等. 抗旱型高粱开花前期和后期应对水分亏缺的生理调节研究 [J]. 山西农业大学学报: 自然科学版, 2020, 40(3): 37-44.
	Wang YQ, Zhang F, Zhu K, et al. Physiological response to water-deficience of drought-tolerant sorghum variety prior to and post of flowering [J]. J Shanxi Agric Univ Nat Sci Ed, 2020, 40(3): 37-44.
[2]	高士杰, 陈冰嬬, 李继洪. 对粒用高粱育种的思考 [J]. 现代农业科技, 2013(10): 31-32, 37.
	Gao SJ, Chen BR, Li JH. Thoughts on breeding of grain sorghum [J]. Mod Agric Sci Technol, 2013(10): 31-32, 37.
[3]	陈冰嬬, 李继洪, 王阳, 等. 高粱(Sorghum bicolor (L.) Moench)种质资源研究进展 [J]. 西北农林科技大学学报: 自然科学版, 2013, 41(1): 67-72, 77.
	Chen BR, Li JH, Wang Y, et al. Advances in germplasm resources of sorghum (Sorghum bicolor (L.) Moench) [J]. J Northwest A&F Univ Nat Sci Ed, 2013, 41(1): 67-72, 77.
[4]	丁延庆, 徐建霞, 汪灿, 等. 基于Super-GBS技术的高粱籽粒酿造相关性状QTL定位 [J]. 核农学报, 2023, 37(2): 241-250.
	Ding YQ, Xu JX, Wang C, et al. QTL mapping of grain traits related to brewing in sorghum based on super-GBS technology [J]. J Nucl Agric Sci, 2023, 37(2): 241-250.
[5]	阳志锐, 冉红艳. 贵州省酱香型白酒全产业链发展现状及能级提升路径研究 [J]. 中国酿造, 2025, 44(3): 285-291.
	Yang ZR, Ran HY. Development status and capacity enhancement path of the whole industry chain of sauce-flavor Baijiu in Guizhou province [J]. China Brew, 2025, 44(3): 285-291.
[6]	Mace ES, Hunt CH, Jordan DR. Supermodels: sorghum and maize provide mutual insight into the genetics of flowering time [J]. Theor Appl Genet, 2013, 126(5): 1377-1395.
[7]	Upadhyaya HD, Reddy KN, Vetriventhan M, et al. Latitudinal adaptation of flowering response to photoperiod and temperature in the world collection of sorghum landraces [J]. Crop Sci, 2018, 58(3): 1265-1276.
[8]	Rooney WL, Aydin S. Genetic control of a photoperiod-sensitive response in Sorghum bicolor (L.) moench [J]. Crop Sci, 1999, 39(2): 397-400.
[9]	Smith CW, Frederiksen RA. Sorghum: Origin, History, Technology, and Production[M]. Wiley, 2000: 240-242.
[10]	Murphy RL, Klein RR, Morishige DT, et al. Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum [J]. Proc Natl Acad Sci USA, 2011, 108(39): 16469-16474.
[11]	Casto AL, Mattison AJ, Olson SN, et al. Maturity2, a novel regulator of flowering time in Sorghum bicolor, increases expression of SbPRR37 and SbCO in long days delaying flowering [J]. PLoS One, 2019, 14(4): e0212154.
[12]	Childs KL, Miller FR, Cordonnier-Pratt MM, et al. The sorghum photoperiod sensitivity gene, Ma3, encodes a phytochrome B [J]. Plant Physiol, 1997, 113(2): 611-619.
[13]	Liu HH, Liu HQ, Zhou LN, et al. Parallel domestication of the heading date 1 gene in cereals [J]. Mol Biol Evol, 2015, 32(10): 2726-2737.
[14]	Murphy RL, Morishige DT, Brady JA, et al. Ghd7 (Ma6) represses sorghum flowering in long days: Ghd7 alleles enhance biomass accumulation and grain production [J]. Plant Genome, 2014, 7(2): plantgenome2013.11.0040.
[15]	Yang SS, Murphy RL, Morishige DT, et al. Sorghum phytochrome B inhibits flowering in long days by activating expression of SbPRR37 and SbGHD7, repressors of SbEHD1, SbCN8 and SbCN12 [J]. PLoS One, 2014, 9(8): e105352.
[16]	Song YH, Ito S, Imaizumi T. Similarities in the circadian clock and photoperiodism in plants [J]. Curr Opin Plant Biol, 2010, 13(5): 594-603.
[17]	Yang MK, Lin WJ, Xu YR, et al. Flowering-time regulation by the circadian clock: From Arabidopsis to crops [J]. Crop J, 2024, 12(1): 17-27.
[18]	Huang XZ, Yang YF, Xu C. Biomolecular condensation programs floral transition to orchestrate flowering time and inflorescence architecture [J]. New Phytol, 2025, 245(1): 88-94.
[19]	Kong WQ, Kim C, Zhang D, et al. Genotyping by sequencing of 393 Sorghum bicolor BTx623×IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection [J]. G3, 2018, 8(8): 2563-2572.
[20]	Ding YQ, Wang YL, Xu JX, et al. A telomere-to-telomere genome assembly of Hongyingzi, a sorghum cultivar used for Chinese Baijiu production [J]. Crop J, 2024, 12(2): 635-640.
[21]	Bangbol Sangma H. Genetic characterization of flowering time in sorghum [D]. Queensland: The University of Queensland, 2013.
[22]	Parh DK. DNA-based markers for ergot resistance in sorghum [D]. Queensland: The University of Queensland, 2005.
[23]	Srinivas G, Satish K, Madhusudhana R, et al. Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum [J]. Theor Appl Genet, 2009, 118(8): 1439-1454.
[24]	Wang XM, Mace E, Hunt C, et al. Two distinct classes of QTL determine rust resistance in sorghum [J]. BMC Plant Biol, 2014, 14: 366.
[25]	Mantilla Perez MB, Zhao J, Yin YH, et al. Association mapping of brassinosteroid candidate genes and plant architecture in a diverse panel of Sorghum bicolor [J]. Theor Appl Genet, 2014, 127(12): 2645-2662.
[26]	Guindo D, Teme N, Vaksmann M, et al. Quantitative trait loci for sorghum grain morphology and quality traits: Toward breeding for a traditional food preparation of West-Africa [J]. J Cereal Sci, 2019, 85: 256-272.
[27]	Reddy RN, Madhusudhana R, Mohan SM, et al. Mapping QTL for grain yield and other agronomic traits in post-rainy sorghum [Sorghum bicolor (L.) Moench [J]. Theor Appl Genet, 2013, 126(8): 1921-1939.
[28]	Upadhyaya HD, Wang YH, Sharma R, et al. SNP markers linked to leaf rust and grain mold resistance in sorghum [J]. Mol Breed, 2013, 32(2): 451-462.
[29]	Feltus FA, Hart GE, Schertz KF, et al. Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations [J]. Theor Appl Genet, 2006, 112(7): 1295-1305.
[30]	Bouchet S, Olatoye MO, Marla SR, et al. Increased power to dissect adaptive traits in global sorghum diversity using a nested association mapping population [J]. Genetics, 2017, 206(2): 573-585.
[31]	Shiringani AL, Frisch M, Friedt W. Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench [J]. Theor Appl Genet, 2010, 121(2): 323-336.
[32]	Olatoye MO, Marla SR, Hu ZB, et al. Dissecting adaptive traits with nested association mapping: genetic architecture of inflorescence morphology in sorghum [J]. G3, 2020, 10(5): 1785-1796.
[33]	Boycheva I, Vassileva V, Revalska M, et al. Cyclin-like F-box protein plays a role in growth and development of the three model species Medicago truncatula, Lotus japonicus, and Arabidopsis thaliana [J]. Res Rep Biol, 2015, 6: 117-130.
[34]	Lechner E, Achard P, Vansiri A, et al. F-box proteins everywhere [J]. Curr Opin Plant Biol, 2006, 9(6): 631-638.
[35]	Kuroda H, Takahashi N, Shimada H, et al. Classification and expression analysis of Arabidopsis F-box-containing protein genes [J]. Plant Cell Physiol, 2002, 43(10): 1073-1085.
[36]	Cheng CH, Wang ZJ, Ren ZY, et al. SCFAtPP2-B11 modulates ABA signaling by facilitating SnRK2.3 degradation in Arabidopsis thaliana [J]. PLoS Genet, 2017, 13(8): e1006947.
[37]	曾冰洁, 阎晋东, 杨飘, 等. 拟南芥ZTL/FKF1/LKP2蛋白家族功能研究进展 [J]. 生物信息学, 2019, 17(3): 145-150.
	Zeng BJ, Yan JD, Yang P, et al. Progress of function studies of ZTL/FKF1/LKP2 proteins family in Arabidopsis [J]. Chin J Bioinform, 2019, 17(3): 145-150.
[38]	Zoltowski BD, Imaizumi T. Structure and function of the ZTL/FKF1/LKP2 group proteins in Arabidopsis [J]. Enzymes, 2014, 35: 213-239.
[39]	Lee HG, Kim J, Park KH, et al. High-temperature-induced FKF1 accumulation promotes flowering through the dispersion of GI and degradation of SVP [J]. Nat Plants, 2025, 11: 1282-1297.
[40]	Hicks KA, Millar AJ, Carré IA, et al. Conditional circadian dysfunction of the Arabidopsis early-flowering 3 mutant [J]. Science, 1996, 274(5288): 790-792.
[41]	Makino S, Kiba T, Imamura A, et al. Genes encoding pseudo-response regulators: insight into his-to-asp phosphorelay and circadian rhythm in Arabidopsis thaliana [J]. Plant Cell Physiol, 2000, 41(6): 791-803.
[42]	Sreekantan L, Mathiason K, Grimplet J, et al. Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning [J]. Plant Mol Biol, 2010, 73(1/2): 191-205.
[43]	Alabadí D, Oyama T, Yanovsky MJ, et al. Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock [J]. Science, 2001, 293(5531): 880-883.
[44]	Quail PH. Phytochrome photosensory signalling networks [J]. Nat Rev Mol Cell Biol, 2002, 3(2): 85-93.
[45]	彭凌涛. 控制拟南芥和水稻开花时间光周期途径的分子机制 [J]. 植物生理学通讯, 2006, 42(6): 1021-1031.
	Peng LT. Molecular mechanism of flowering time controlling photoperiod pathway in Arabidopsis and rice [J]. Plant Physiol Commun, 2006, 42(6): 1021-1031.
[46]	贺军虎, 李唯正, 陈华蕊, 等. ‘金煌’杧果MiCAB2的克隆及表达与花期调控关系分析 [J]. 园艺学报, 2017, 44(7): 1275-1286.
	He JH, Li WZ, Chen HR, et al. Cloning of the light harvesting chlorophyll a/b binding protein gene (MiCAB2) from ‘Jinhuang’ mango, and correlation analysis between its expression and flowering regulation [J]. Acta Hortic Sin, 2017, 44(7): 1275-1286.
[47]	Zhao YG, Kong H, Guo YL, et al. Light-harvesting chlorophyll a/b-binding protein-coding genes in Jatropha and the comparison with Castor, cassava and Arabidopsis [J]. PeerJ, 2020, 8: e8465.
[48]	阳江华, 张希财, 邹智. 橡胶树捕光叶绿素a/b结合蛋白基因CAB2的克隆与分析 [J]. 西南林业大学学报: 自然科学, 2019, 39(1): 88-94.
	Yang JH, Zhang XC, Zou Z. Molecular cloning and analysis of HbCAB2, a chlorophyll a/b-binding protein-encoding gene from Hevea brasiliensis [J]. J Southwest For Univ Nat Sci, 2019, 39(1): 88-94.
[49]	Zou Z, Li MY, Jia RZ, et al. Genes encoding light-harvesting chlorophyll a/b-binding proteins in papaya (Carica papaya L.) and insight into lineage-specific evolution in Brassicaceae [J]. Gene, 2020, 748: 144685.
[50]	孔德元. 光周期调控甘菊成花过程中ClRVE基因家族功能分析 [D]. 北京: 北京林业大学, 2022.
	Kong DY. Functional analysis of ClRVE gene family during photoperiod regulation of chamomile flower formation [D]. Beijing: Beijing Forestry University, 2022.
[51]	Mishal R, Luna-Arias JP. Role of the TATA-box binding protein (TBP) and associated family members in transcription regulation [J]. Gene, 2022, 833: 146581.

引物名称 Primer name	orward primer （5′‒3′）正向引物 F	everse primer （5′‒3′）反向引物 R
V1f1	CAACTTCAGTGCAACGGTCG	AGCAAGGATTGTGTGGTGCT
V423	TCAGTGCAACGGTCGACAAA	TGAATGGTGAACAGCCGACC
Hd8800	CACATCAGTGTGTGCCGTTG	TTAGGGGCGTTCTTCTGCTC
V5f1	CATCCACGGGGTTGAAGTCT	AGCGGTCCATTGCTCAAAGT

引物名称 Primer name	orward primer （5′‒3′）正向引物 F	everse primer （5′‒3′）反向引物 R
V1f1	CAACTTCAGTGCAACGGTCG	AGCAAGGATTGTGTGGTGCT
V423	TCAGTGCAACGGTCGACAAA	TGAATGGTGAACAGCCGACC
Hd8800	CACATCAGTGTGTGCCGTTG	TTAGGGGCGTTCTTCTGCTC
V5f1	CATCCACGGGGTTGAAGTCT	AGCGGTCCATTGCTCAAAGT

样本Sample	平均测序深度Mean depth （X）	短片段总数Number of total Reads	总碱基读数Clean bases （bp）	GC （%）	Q30 （%）	比对Mapped reads （%）
红缨子	67.04	369 858 258	55 478 738 700	44.63	91.96	99.41
SAP001	70.27	355 144 466	53 271 669 900	43.54	96.28	98.88
晚熟池	77.31	387 856 226	58 178 433 900	43.67	97.29	99.34
早熟池	86.91	443 492 672	66 523 900 800	43.53	97.36	98.95

样本Sample	平均测序深度Mean depth （X）	短片段总数Number of total Reads	总碱基读数Clean bases （bp）	GC （%）	Q30 （%）	比对Mapped reads （%）
红缨子	67.04	369 858 258	55 478 738 700	44.63	91.96	99.41
SAP001	70.27	355 144 466	53 271 669 900	43.54	96.28	98.88
晚熟池	77.31	387 856 226	58 178 433 900	43.67	97.29	99.34
早熟池	86.91	443 492 672	66 523 900 800	43.53	97.36	98.95

基因 Gene	变异位置 Variation position （bp）	参考基因组 Reference	等位变异Alternative	CDS突变类型Type of CDS mutation	启动子突变Promoter mutation
SbiHYZ.03G216400	59 930 660	A	-	-	碱基缺失
SbiHYZ.03G216700	59 972 784	C	A	非同义突变
SbiHYZ.03G216800	59 974 642	C	A	-	碱基突变
SbiHYZ.03G216900	59 980 499	A	-	缺失突变/移码
	59 980 657	G	A	非同义突变
	59 980 792	G	T	非同义突变
	59 980 816	G	C	非同义突变
SbiHYZ.03G217000	60 060 314	A	-	-	碱基缺失
SbiHYZ.03G217200	60 093 586	A	C	非同义突变
SbiHYZ.03G217700	60 140 432	G	A	非同义突变
SbiHYZ.03G218800	60 365 936	C	T	-	碱基突变
SbiHYZ.03G218900	60 375 442	C	T	非同义突变