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棉花作为全球重要的经济农作物,是最多的天然纤维来源,被广泛应用于织造行业. 栽培棉花多为异源四倍体,由两个异源二倍体棉属经A基因组与D基因组杂交后染色体加倍形成[1]. 陆地棉(Gossypium hirsutum)作为最重要的异源四倍体棉种占领了超过全球95%的棉花市场. 产量和纤维品质是棉花研究中最受关注的部分[2],但棉花产量与纤维品质呈负相关,难以同时改良[3],是培育优异棉种的巨大挑战. 棉花产量及纤维品质作为数量性状,受多个基因控制. 探究棉花产量与纤维品质的遗传决定因素,利用分子标记检测来为目的基因定位提供依据,对棉花品质改良具有重要意义. 由于陆地棉种内杂交多态性低,因此构建高密度的陆地棉种内遗传图谱是其分子标记辅助选择育种的关键.
构建高密度遗传图谱需要寻找众多的分子标记. 简单序列重复(Simple sequence repeat,SSR)标记分布多且广,实验重复性好且结果可靠,可以在等位基因间显示多个差异[4-5]. 简化基因组测序(Specific locus amplified fragment sequencing,SLAF-seq)是在高通量测序的背景下发展起来的[6-7]. SLAF-seq的3个显著优势是:深度测序保证了基因分型准确;测序成本低;正式测序前利用预测系统提升标记效率. SLAF-seq近年来已被广泛用于单核苷酸多样性(Single nucleotide polymorphism,SNP)检测[8-11].
数量性状位点(Quantitative trait loci,QTL)是在调控生物体数量性状中起重要作用的基因片段在染色体上的位置,数量性状不仅受多个QTL的影响,也与环境互作相关,部分数量性状存在一个主效基因对该性状的控制起主导作用,农作物的产量性状一般为数量性状. 对棉花而言,产量性状、纤维品质和抗逆性等都是数量性状. CottonQTLdb搜集了大量来自全球棉花纤维品质、产量性状、抗病性、耐盐等各类性状的QTL,在release 2.3版本中囊括了截至2018年1月来自156个刊物的4 892个QTL[12-13];Ijaz等[14]总结了2017-2019年多个研究者定位的、与纤维品质相关的稳定QTL.
本研究运用SLAF-seq SNP技术结合SSR分子标记构建高密度遗传图谱,帮助增加遗传图谱的准确性,缩小了QTL长度区间,使QTL定位更加准确高效,可有效推进后续精细定位群体选择和候选基因筛选,为陆地棉产量和纤维品质的分子育种提供参考.
QTL Mapping of Yield and Fiber Quality Traits in an Upland Cotton RIL Population
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摘要: 棉花是世界首要的天然纤维作物,同时也是重要的蛋白和油料作物. 该研究构建了一个包含184个单株的(渝棉1号×超早3号)重组近交系群体. 利用SSR和SLAF-seq SNP分子标记共同构建高密度遗传图谱,结合多种环境鉴定产量和纤维品质性状表型,定位棉花产量和纤维品质性状的QTL. 研究结果表明:①对8 020个SSR与SNP标记进行遗传连锁分析,构建的遗传图谱共2 945个位点(41 SSR和2 904 SNP),遗传长度为4 650.71 cM,覆盖陆地棉基因组总长的98.30%;②共定位到76个QTL,包括35个产量性状QTL,41个纤维品质性状QTL,LOD值分布在2.50~7.76之间,解释表型变异率为6.4%~23.4%;③ 10个QTL在两个及以上环境被检测到,为环境稳定QTL.Abstract: Cotton is the leading natural fiber crop, and also an important protein crop and oil crop in the world. A RIL population consisting of 184 lines (Yumian 1 × Chaozao 3) was constructed in this study. The SNP markers obtained by SLAF-seq and polymorphic SSR markers were used to construct a high-density genetic map. The phenotypic data of yield and fiber quality traits detected in multiple environments were used to locate QTL for yield and fiber quality traits. The results are as follows: ① Linkage analysis was conducted on 8 020 markers, and a genetic map containing 2 945 (41 SSR and 2 904 SNP) loci were finally constructed. The genetic length of the constructed map was 4 650.71 cM, and covered 98.30% of the upland cotton genome. ② Totally, 35 QTLs for yield traits and 41 QTLs for fiber quality traits were detected, which explained 6.4% to 23.4% of the phenotypic variation, and their LOD value ranged from 2.50 to 7.76. ③ Ten QTLs were detected in two or more environments, which were environment-stable QTL.
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Key words:
- upland cotton /
- SLAF-seq SNP /
- yield /
- fiber quality /
- QTL /
- genetic map .
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表 1 4个环境间产量与纤维品质的方差分析
性状 变异来源于基因型 变异来源于环境 籽指(SI) 2.90** 22.93** 衣分(LP) 2.58** 247.41** 铃质量(BW) 1.82** 259.13** 衣指(LI) 1.66** 148.50** 纤维长度(FL) 3.20** 99.73** 整齐度(FU) 1.60** 19.60** 断裂比强度(FS) 2.11** 67.90** 马克隆值(FM) 1.92** 24.43** 伸长率(FE) 1.82** 63.08** 注:**表示p<水平差异具有统计学意义;方差分析时筛除了缺失数据. 表 2 亲本及RIL群体的产量和纤维品质性状表现
性状 环境 亲本 群体 P1 P2 均值 标准差 峰度 偏度 变异系数/% 籽指/g CQ 10.42 7.68 9.60 1.21 0.88 -0.35 12.65 HN 9.97 9.76 9.59 0.97 0.47 0.64 10.06 KL - 9.74 9.59 0.88 0.19 0.26 9.13 KT 9.26 9.75 10.19 1.00 0.48 0.33 9.79 衣分/% CQ 43.58 39.74 39.65 0.03 2.21 -1.04 7.67 HN 42.77 40.07 43.49 0.02 3.43 -1.22 5.61 KL - 42.82 43.74 0.02 0.49 -0.74 5.14 KT 44.36 44.77 45.52 0.02 0.26 -0.33 3.89 铃质量/g CQ 4.63 2.89 4.31 0.82 0.63 -0.01 19.05 HN 6.19 6.57 5.91 0.64 1.53 0.62 10.79 KL - 5.52 5.81 0.83 7.42 1.20 14.34 KT 5.81 5.35 6.11 0.71 0.20 0.44 11.59 衣指/g CQ 8.04 5.05 6.53 0.89 0.43 -0.02 13.62 HN 6.23 5.99 7.18 0.85 1.69 0.63 11.90 KL - 7.13 7.41 0.89 0.59 0.03 12.08 KT - 6.99 8.61 1.00 -0.26 0.40 11.39 长度/mm CQ 29.20 25.65 27.99 1.25 -0.33 -0.01 4.48 HN 25.00 24.70 26.04 1.09 1.21 0.30 4.20 KL - 28.30 27.65 1.13 0.21 -0.15 4.10 KT 27.90 25.80 27.43 1.09 -0.09 0.00 3.97 整齐度/% CQ 84.20 82.25 83.27 1.45 0.86 -0.78 1.74 HN 82.00 82.30 82.71 1.32 -0.03 -0.35 1.60 KL - 82.80 83.86 1.29 -0.18 -0.18 1.54 KT 82.30 79.30 82.72 1.29 -0.23 -0.01 1.56 比强度/(cN·tex-1) CQ 36.85 26.25 29.94 2.32 0.05 0.32 7.74 HN 27.00 23.30 27.20 1.87 0.56 0.44 6.88 KL - 27.90 30.06 1.79 -0.42 -0.05 5.95 KT 32.20 24.20 28.67 1.76 -0.22 0.23 6.13 马克隆值 CQ 4.45 3.95 4.77 0.71 -0.80 -0.32 14.91 HN 5.00 5.00 4.91 0.36 -0.23 -0.14 7.31 KL - 4.70 5.05 0.33 0.33 -0.55 6.59 KT 4.80 5.70 5.20 0.35 1.57 -0.92 6.66 伸长率/% CQ 6.75 6.60 6.67 0.06 -0.47 0.23 0.94 HN 6.70 6.70 6.69 0.05 2.49 -0.08 0.78 KL - 6.50 6.61 0.11 -0.09 -0.31 1.64 KT 6.80 6.60 6.72 0.07 0.01 0.02 1.08 注:P1:渝棉1号;P2:超早3号;渝棉1号中“-”表示性状缺失. 表 3 遗传图谱标记在染色体上的分布情况
染色体 标记数量 位点数量 遗传距离/cM 物理长度/bp 覆盖率/% A01 286 126 183.30 117 016 704 99.02 A02 231 94 163.71 107 333 900 99.13 A03 198 137 212.77 111 229 457 99.68 A04 169 97 150.78 86 053 755 98.12 A05 240 108 218.21 108 400 853 97.79 A06 220 76 100.77 123 462 163 97.61 A07 399 141 208.90 92 981 754 96.26 A08 456 124 215.88 124 039 941 99.19 A09 354 141 201.29 81 719 658 98.20 A10 384 137 172.40 114 841 377 99.78 A11 244 126 220.73 120 246 152 99.07 A12 157 98 184.22 105 421 784 97.99 A13 695 120 182.31 107 195 460 97.13 D01 140 84 146.26 64 371 629 99.50 D02 338 126 177.79 68 788 196 98.58 D03 150 61 107.03 52 577 860 97.55 D04 188 113 168.80 54 021 011 94.88 D05 229 140 228.25 63 394 453 99.16 D06 835 102 114.59 64 834 129 99.04 D07 562 185 213.82 56 925 557 97.45 D08 469 76 139.82 67 705 273 98.01 D09 127 89 169.30 51 108 213 98.28 D10 277 116 160.11 64 306 655 96.15 D11 158 84 196.97 70 262 715 98.46 D12 201 100 220.63 61 138 199 99.10 D13 313 144 192.06 63 570 579 98.64 表 4 在两个及以上环境中存在的QTL
QTL名称 环境 LOD值 邻近标记 物理位置/bp 置信区间/cM 解释变异/% 加性效应 qSI-A08-1 HN 6.73 Marker15151 119 717 554 172.41~181.15 16.4 0.43 KT 2.56 Marker15165 120242792 161.89~181.15 6.5 0.32 qBW-A12-1 HN 2.70 Marker22087 83 891 639 72.37~98.11 6.9 -0.22 KT 3.19 Marker22081 83322110 79.46~93.88 8.2 -0.19 qFL-A03-1 KL 2.96 Marker3847 3 744 087 30.11~34.68 8.1 -0.38 HN 4.03 Marker3837 3523985 30.11~41.78 10.2 -0.41 qFL-A10-2 HN 3.29 Marker18622 85 389 212 68.32~84.07 8.4 -0.38 KT 2.91 Marker18759 99459952 63.70~71.94 7.4 -0.34 qFL-D11-1 CQ 7.76 Marker45630 23 731 197 79.02~92.51 23.4 -0.70 KL 4.89 Marker45687 24033412 79.02~91.60 13.0 -0.48 HN 3.49 Marker45687 24033412 84.12~92.07 8.9 -0.39 KT 4.42 Marker45670 23965331 84.12~91.60 11.0 -0.43 qFM-D07-1 CQ 5.93 SWU10410 19 999 192 89.09~102.77 18.7 -0.35 KT 3.28 Marker37683 20043530 93.56~97.72 8.3 -0.11 qFS-A03-1 KL 2.67 NAU3995 3 941 065 30.11~34.68 7.3 -0.59 HN 3.88 Marker3837 3523985 30.11~40.31 9.9 -0.68 qFS-D13-1 KL 2.76 Marker49416 58 703 007 157.35~171.28 7.6 -0.56 KT 3.08 Marker49441 60385784 164.44~186.91 7.8 -0.55 qFE-A09-1 KL 3.24 Marker17078 77 045 685 149.66~152.63 8.8 0.04 KT 3.01 Marker17045 75849690 139.42~151.88 7.6 0.02 qFE-A10-1 CQ 3.32 Marker18363 72 266 619 92.62~99.95 10.8 -0.02 KT 2.50 Marker18622 85389212 68.32~79.60 6.4 -0.02 -
[1] WENDEL J F. New World Tetraploid Cotton Contain Old World Cytoplasm[J]. Proe. Natl. Aead. Sei. USA, 1989, 86(11): 4132-4136. doi: 10.1073/pnas.86.11.4132 [2] 金宇豪, 阳会兵, 高倩文, 等. 陆地棉纤维品质和农艺性状遗传多样性分析及优良材料鉴定[J]. 东北农业大学学报, 2022, 53(2): 1-12. doi: https://www.cnki.com.cn/Article/CJFDTOTAL-DBDN202202001.htm [3] GU Q S, KE HF, LIU Z W, et al. A High-Density Genetic Map and Multiple Environmental Tests Reveal Novel Quantitative Trait Loci and Candidate Genes for Fibre Quality and Yield in Cotton[J]. Theoretical and Applied Genetics, 2020, 133(12): 3395-3408. doi: 10.1007/s00122-020-03676-z [4] NIE G, HUANG T, MA X, et al. Genetic Variability Evaluation and Cultivar Identification of Tetraploid Annual Ryegrass Using SSR Markers[J]. PeerJ, 2019, 7: e7742. doi: 10.7717/peerj.7742 [5] WU Y Z, HUANG L Y, ZHOU D Y, et al. Development and Application of Perfect SSR Markers in Cotton[J]. Journal of Cotton Research, 2020, 3(1): 207-214. [6] SUN X, LIU D, ZHANG X, et al. SLAF-seq: an Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing[J]. Plos One. 2013, 8(3): e58700. doi: 10.1371/journal.pone.0058700 [7] ZHANG J, ZHANG Q X, CHENG T R, et al. High-Density Genetic Map Construction and Identification of a Locus Controlling Weeping Trait in an Ornamental Woody Plant (Prunus Mume Sieb. et Zucc)[J]. DNA Research, 2015, 22(3): 183-191. doi: 10.1093/dnares/dsv003 [8] ZHANG K, KURAPARTHY V, FANG H, et al. High-Density Linkage Map Construction and QTL Analyses for Fiber Quality, Yield and Morphological Traits Using Cottonsnp63k Array in Upland Cotton (Gossypium hirsutum L.)[J]. BMC Genomics, 2019, 20(1): 889. doi: 10.1186/s12864-019-6214-z [9] NIU S F, ZHAI Y, WU R X, et al. Development and Characterization of 33 Polymorphic Microsatellite Markers in Trachurus Japonicus by SLAF‐Seq Technology[J]. Journal of Applied Ichthyology, 2021, 37(2): 308-313. doi: 10.1111/jai.14158 [10] REN H L, HAN J N, WANG X R, et al. QTL Mapping of Drought Tolerance Traits in Soybean With SLAF Sequencing[J]. The Crop Journal, 2020, 8(6): 977-989. doi: 10.1016/j.cj.2020.04.004 [11] HUANG KY, SHI Y L, PAN G, et al. Genome-Wide Association Analysis of Fiber Fineness and Yield in Ramie (Boehmeria Nivea) Using SLAF-Seq[J]. Euphytica, 2021, 217(2): 1-16. [12] SAID J I, KNAPKA J A, SONG M Z, et al. Cotton QTLdb: A Cotton QTL Database for QTL Analysis, Visualization, and Comparison Between Gossypium hirsutum and G. hirsutum×G. barbadense Populations[J]. Molecular Genetics and Genomics, 2015, 290(4): 1615-1625. doi: 10.1007/s00438-015-1021-y [13] SAID J I, LIN Z X, ZHANG X L, et al. A Comprehensive Meta QTL Analysis for Fiber Quality, Yield, Yield Related and Morphological Traits, Drought Tolerance, and Disease Resistance in Tetraploid Cotton[J]. BMC Genomics, 2013, 14: 776. doi: 10.1186/1471-2164-14-776 [14] IJAZ B, ZHAO N, KONG J, et al. Fiber Quality Improvement in Upland Cotton (Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application[J]. Front Plant Sci. 2019, 10: 1585. doi: 10.3389/fpls.2019.01585 [15] ZHANG Z S, XIAO Y H, LUO M, et al. Construction of a Genetic Linkage Map and QTL Analysis of Fiber-Related Traits in Upland Cotton(Gossypium hirsutum L.)[J]. Euphytica, 2005, 144(1/2): 91-99. [16] 王文文. 陆海种间图谱加密与染色体结构变异分析[D]. 重庆: 西南大学, 2017. [17] WANG B H, ZHUANG Z M, ZHANG Z S, et al. Advanced Backcross QTL Analysis of Fiber Strength and Fineness in a Cross Between Gossypium hirsutum and G. mustelinum Frontiters In Plant[J]. Frontiers in Plant Science, 2017, 8: 1848. doi: 10.3389/fpls.2017.01848 [18] PATERSON A H, WENDEL J F, GUNDLACH H, et al. Repeated Polyploidization of Gossypium Genomes and the Evolution of Spinnable Cotton Fibres[J]. Nature, 2012, 492(7429): 423-427. doi: 10.1038/nature11798 [19] SOULARD L, MOURNET P, GUITTON B, et al. Construction of Two Genetic Linkage Maps of Taro Using Single Nucleotide Polymorphism and Microsatellite Markers[J]. Molecular Breeding, 2017, 37: 1-15. doi: 10.1007/s11032-016-0586-4 [20] KOSAMBI D D. The Estimation of Map Distances From Recombination Values[M]. New Delhi: Springer India, 2016. [21] LI F, FAN G, LU C, et al. Genome Sequence of Cultivated Upland Cotton (Gossypium hirsutum TM-1) Provides Insights into Genome Evolution[J]. Nat Biotechnol, 2015, 33(5): 524-530. doi: 10.1038/nbt.3208 [22] ZHANG T Z, HU Y, JIANG W K, et al. Sequencing of Allotetraploid Cotton (Gossypium hirsutum) Provides a Resource for Fiber Improvement[J]. Nature Biotechnology, 2015, 33(5): 531-537. doi: 10.1038/nbt.3207 [23] 潘凤英, 刘露露, 郭泽西, 等. 华东葡萄遗传连锁图谱构建及灰霉病抗性QTL定位[J]. 南方农业学报, 2020, 53(9): 2383-2391. doi: https://www.cnki.com.cn/Article/CJFDTOTAL-GXNY202209001.htm [24] 王怡悦, 刘红, 徐姚. 以2b-RAD技术构建凡纳滨对虾遗传图谱及生长性状QTL定位[J]. 南方农业学报, 2020-09-06(网络首发), http://kns.cnki.net/kcms/detail/45.1381.S.20220905.1529.008.html. [25] FAN Z, WANG K, RAO J, et al. Interactions Among Multiple Quantitative Trait Loci Underlie Rhizome Development of Perennial Rice[J]. Frontiers in Plant Science, 2020, 11: 1-10. doi: 10.3389/fpls.2020.00001 [26] LIU W, SONGC, REN Z. Genome-wide Association Study Reveals the Genetic Basis of Fiber Quality Traits in Upland Cotton (Gossypium hirsutum L.)[J]. BMC Plant Biology, 2020, 20(1): 1-13. doi: 10.1186/s12870-019-2170-7 [27] DENG J, XIE X L, WANG D F, et al. Paternal Origins and Migratory Episodes of Domestic Sheep[J]. Current Biology, 2020, 30(20): 4085-4095. doi: 10.1016/j.cub.2020.07.077 [28] SHAHEEN T, ZAFAR Y, RAHMAN M, et al. QTL Mapping of Some Productivity and Fibre Traits in Gossypium arboreum[J]. Turkish Journal of Botany, 2013, 37: 802-810. doi: 10.3906/bot-1209-47 [29] NOORMOHAMMADI Z, HASHEMINEJAD-AHANGARANI FARAHANI Y, SHEIDAI M, et al. Genetic Diversity Analysis in Opal Cotton Hybrids Based on SSR, ISSR, and RAPD Markers[J]. Genetics and Molecular Research, 2013, 12(1): 256-269. doi: 10.4238/2013.January.30.12 [30] 张正圣. 陆地棉遗传连锁图谱的构建与纤维相关性状的QTL分析[D]. 重庆: 西南农业大学, 2005. [31] ZHANG S W, WANG T, LIU Q, et al. Quantitative Trait Locus Analysis of Boll-Related Traits in an Intraspecific Population of Gossypium hirsutum[J]. Euphytica, 2015, 203(1): 121-144. doi: 10.1007/s10681-014-1281-3 [32] ABDELRAHEEM A, FANG D D, DEVER J, et al. QTL Analysis of Agronomic, Fiber Quality, and Abiotic Stress Tolerance Traits in a Recombinant Inbred Population of Pima Cotton[J]. Crop Science, 2020, 60(4): 1823-1843. doi: 10.1002/csc2.20153 [33] LARSON S, DEHAAN L, POLANDJ, et al. Genome Mapping of Quantitative Trait Loci (QTL) Controlling Domestication Traits of Intermediate Wheatgrass (Thinopyrum intermedium)[J]. Theoretical and Applied Genetics, 2019, 132(8): 2325-2351. doi: 10.1007/s00122-019-03357-6 [34] YI Q, LIU Y H, HOU X B, et al. Genetic Dissection of Yield-Related Traits and Mid-Parent Heterosis for Those Traits in Maize (Zea mays L.)[J]. BMC Plant Biology, 2019, 19(1): 1-20. doi: 10.1186/s12870-018-1600-2 [35] ULLOA M, SAHA S, JENKINS J N, et al. Chromosomal Assignment of RFLP Linkage Groups Harboring Important QTLs on an Intraspecific Cotton (Gossypium hirsutum L.) JoinMap[J]. Journal of Heredity, 2004, 96(2): 132-144. [36] RONG J K, FELTUS F A, WAGHMARE V N, et al. Meta-analysis of Polyploid Cotton QTL Shows Unequal Contributions of Subgenomes to a Complex Network of Genes and Gene Clusters Implicated in Lint Fiber Development[J]. Genetics, 2007, 176(4): 2577-2588.