全基因組關(guān)聯(lián)分析饅頭比容與質(zhì)構(gòu)SNP標(biāo)記

1、全基因組關(guān)聯(lián)分析饅頭比容與質(zhì)構(gòu)S N P標(biāo)記劉娟1陳廣鳳2田紀(jì)春3吳澎1趙子彤1楊藝1李向陽(yáng)1唐曉珍1(山東省高校食品加工技術(shù)與質(zhì)量限制重點(diǎn)實(shí)驗(yàn)室；山東農(nóng)業(yè)大學(xué)食品學(xué)院 1,泰安 271018)(德州學(xué) 院生態(tài)與景觀學(xué)院2,德州 253023)(山東農(nóng)業(yè)大學(xué)小麥品質(zhì)育種研究室；山東省作物生物學(xué)重點(diǎn)實(shí)驗(yàn)室3,泰安 271018)摘要為從分子水平研究限制饅頭比容與質(zhì)構(gòu)性狀的基因位點(diǎn),以 205份不同小麥品種為實(shí)驗(yàn)材料,利 用分布于小麥全基因組的 24 355個(gè)單核昔酸多態(tài)性(SNP標(biāo)記對(duì)饅頭比容與質(zhì)構(gòu)性狀進(jìn)行關(guān)聯(lián)分析.共 檢測(cè)到42個(gè)比容性狀顯著關(guān)聯(lián)位點(diǎn),其中8個(gè)極顯著關(guān)聯(lián)位點(diǎn)(P< 1),

2、同時(shí)也是高遺傳奉獻(xiàn)率位點(diǎn)(F2>10% , 2個(gè)位點(diǎn)至少在兩個(gè)環(huán)境中穩(wěn)定表達(dá)；檢測(cè)到 313個(gè)質(zhì)構(gòu)性狀顯著關(guān)聯(lián)位點(diǎn),其中 31個(gè)極顯著關(guān)聯(lián)位點(diǎn), 46個(gè)高遺傳奉獻(xiàn)率位點(diǎn),11個(gè)位點(diǎn)至少在兩個(gè)環(huán)境中穩(wěn)定表達(dá).同時(shí),開(kāi)掘了 5個(gè)質(zhì)構(gòu)性狀主效關(guān)聯(lián)位點(diǎn),如3B染色體上黏聚性關(guān)聯(lián)位點(diǎn)Kukri_c13329_800等.本研究所得到的這些標(biāo)記為在分子水平上研究饅頭品質(zhì)性狀提供了有價(jià)值的參考.關(guān)鍵詞饅頭比容饅頭質(zhì)構(gòu)單核音酸多態(tài)性標(biāo)記全基因組關(guān)聯(lián)分析顯著關(guān)聯(lián)位點(diǎn)中圖分類號(hào)：文獻(xiàn)標(biāo)識(shí)碼：AGenome-WideAssociation Analysis between SNPMarkers and Spec

3、ific volume and Texture Related Traits of Steamed BreadLIU Juan 1, CHEN Guangfeng 2, TIAN Jichun3, WU Peng 二 ZHAO Zitong 1, YANG Yi 1,LI Xiangyang 1, TANG Xiaozhen 1(Key Laboratory of Food Processing Technology and Quality Control in Shandong Province ； College of Food Science and Engineering, Shand

4、ong Agricultural University 1, Taian 271018) (College of Ecology and Landscape Architecture, Dezhou University 2, Dezhou 253023) (State Key Laboratory of Crop Biology ； Group of Quality Wheat Breading, Shandong Agricultural University3, Taian271018)Abstract In order to study the gene loci that contr

5、ol specific volume and texture of steamed bread, 205 diverse wheat varieties were used to conduct trait-markers association using24 355single nucleotide polymorphism (SNP) markers covered the whole genome of wheat. In the results, 42 significant markers were detected for specific volume of steamed b

6、read distributed across 7 chromosomes of wheat, including 8 highly significant markers (P< 1), as well as high geneticcontribution markers (R2>10%), 2 markers detected in two or more environment. 313 significantmarkers were detected for texture traits of steamed bread mapped onto 15 chromosome

7、s of wheat, including 31 highly associated markers( P< 1), 46 high genetic contribution markers and 11 stablemarkers. At the same time, 5 main sites were detected for texture of steamed bread, such as Kukri_c13329_800 on chromosome 3B. These results will facilitate further researches in sensory p

8、roperties in steamed bread. 1Key words bread specific volume, bread texture, single nucleotide polymorphism markers, genome-wide association analysis, significant markers饅頭的比容和質(zhì)構(gòu)性狀作為影響?zhàn)z頭感官品質(zhì)和市場(chǎng)銷售的重要指標(biāo),一直以來(lái)都是饅頭加工或品質(zhì)改進(jìn)研究的熱點(diǎn)領(lǐng)域,目前對(duì)于饅頭比容和質(zhì)構(gòu)的研究多傾向于原料、 添加劑以及小麥顆粒度等方 面I" ,對(duì)加工技術(shù)的研究多于根底研究.小麥?zhǔn)钱愒戳扼w作物, 因而對(duì)其

9、基因的研究相較于玉米 、水稻8等較晚,但近幾年檢測(cè)手 段的進(jìn)步,使得對(duì)小麥農(nóng)藝性狀及品質(zhì)性狀的的基因研究日趨完善, 但對(duì)小麥類產(chǎn)品如饅頭、面條等感官性狀的基因研究尚鮮見(jiàn)報(bào)道.隨著當(dāng)前單核甘酸多態(tài)性SNP標(biāo)記研究的快速開(kāi)展,以及測(cè) 序技術(shù)和基因芯片技術(shù)的開(kāi)展,自動(dòng)化程度更高的第3代SNPfe記已 迅速取代SSRRFL畤傳統(tǒng)標(biāo)記,成為最具有開(kāi)展?jié)摿Φ姆肿訕?biāo)記9. SNFfe記遺傳穩(wěn)定、數(shù)量多、分布廣且易于檢測(cè)的特點(diǎn)使其能滿足全 基因組關(guān)聯(lián)分析對(duì)大樣本、高密度標(biāo)記的要求,適合于數(shù)量龐大的檢 測(cè)分析,可極大的提升關(guān)聯(lián)分析的效力10-11,現(xiàn)已廣泛應(yīng)用于小麥遺 傳連鎖圖譜的構(gòu)建12-14、分子標(biāo)記輔助育

10、種15-17、遺傳分析和物種進(jìn)基金工程：山東省重點(diǎn)研發(fā)方案公益類2021GNC10101山東農(nóng)業(yè)大學(xué)作物生物學(xué)國(guó)家重點(diǎn)實(shí)驗(yàn)室開(kāi)放課題2021KF14收稿日期：2021-10-09作者簡(jiǎn)介：劉娟,女,1994年出生,碩士,食品科學(xué)通訊 吳澎,女,1972年出生,副教授,食品平安與質(zhì)量限制田紀(jì)春,男,1953年出生,教授,小麥作物育種化等研究方面18-20.本研究以205份不同小麥品種為實(shí)驗(yàn)材料,通過(guò) 全基因組關(guān)聯(lián)分析以求找到與饅頭比容和質(zhì)構(gòu)緊密關(guān)聯(lián)的SNPfe記,為從分子層面研究饅頭品質(zhì)性狀提供有價(jià)值的參考.1 材料與方法實(shí)驗(yàn)材料與表型鑒定205份不同小麥品種,其中203份來(lái)自于中國(guó)十個(gè)種植冬小

11、麥的 省份,包括山東138份、河南24份、河北14份、安徽8份、71蘇6 份、北京5份、陜西4份、甘肅2份、貴州與寧夏分別1份；剩余2 份分別來(lái)自法國(guó)與墨西哥.其中,骨干親本132份,高代品系73份, 高代品系均來(lái)源于山東省.在2021年和2021年間分別將試驗(yàn)材料種植于山東泰安山東農(nóng) 業(yè)大學(xué)和山東德州德州市農(nóng)業(yè)科學(xué)院,播種時(shí)每份材料播種三 行,行長(zhǎng)2 m,行間距m,均勻播種70粒.在小麥生長(zhǎng)期間,對(duì)其 進(jìn)行常規(guī)的田間治理,沒(méi)有出現(xiàn)嚴(yán)重的病蟲害及倒伏現(xiàn)象. 待小麥成 熟后將其進(jìn)行收割、標(biāo)記并研磨成粉.饅頭的制作參考周素梅21等人 的方法并略做改進(jìn).待饅頭冷卻后開(kāi)始測(cè)量饅頭的質(zhì)量、體積與質(zhì)構(gòu).

12、饅頭的體積采用菜籽置換法測(cè)量, 體積與質(zhì)量之比即為比容22;體積 測(cè)量結(jié)束后,用切割機(jī)將饅頭沿豎直方向平行切割成三片, 取中間片 于質(zhì)構(gòu)儀上,在TPA模式下采用P35探頭進(jìn)行壓縮實(shí)驗(yàn)沖,測(cè)試前速 率mm/s,測(cè)試速率mm/s,測(cè)試后速率 mm/s,下壓程度 50%第一次壓縮結(jié)束后,探頭回到起始位置,等待 3s后進(jìn)行第二次壓縮.并采用軟件統(tǒng)計(jì)分析所得數(shù)據(jù).DNA提取和90K SNP芯片分型根據(jù)稍作改動(dòng)的Triticarte 方法提取小麥幼葉中DNA并用 的瓊脂糖電泳對(duì)提取到的DNAt行濃度與質(zhì)量的檢測(cè).委托加利弗尼 亞大學(xué)生物技術(shù)檢測(cè)中央,使用最新開(kāi)發(fā)的90K基因芯片含81 587 個(gè)SNP對(duì)實(shí)

13、9材料DNAS行分型,并利用 GenomeStudio軟件對(duì)分 型結(jié)果進(jìn)行讀取及保存.為保證得到的基因數(shù)據(jù)的質(zhì)量,用plink24 對(duì)基因數(shù)據(jù)進(jìn)行處理,選取檢出率大于和低頻基因頻率大于的 SNP示 記,最終得到24 355個(gè)SN即于饅頭比容和質(zhì)構(gòu)關(guān)聯(lián)分析.在參照 Wan&5等整合的遺傳圖譜的根底上,得到本實(shí)驗(yàn)群體的 SNPM合遺傳圖譜信息.表1.表1 SNP復(fù)合遺傳圖譜信息染色體連鎖群長(zhǎng)度/cM染色體連鎖群長(zhǎng)度/cM染色體連鎖群長(zhǎng)度/cM1A15061B23901D6292A14622B19772D7693A11543B16283D3314A11454B8824D785A12435B2

14、1875D2406A14636B17866D2347A15507B14717D230總計(jì)24355性狀與標(biāo)記間的關(guān)聯(lián)分析運(yùn)用TASSEL軟件中的MLMJI型對(duì)饅頭比容及質(zhì)構(gòu)性狀與標(biāo)記之 間進(jìn)行關(guān)聯(lián)分析,當(dāng)結(jié)果中關(guān)聯(lián)標(biāo)記的P<時(shí),認(rèn)為該標(biāo)記與目標(biāo)性狀存在顯著關(guān)聯(lián)；P< 1時(shí),認(rèn)為標(biāo)記與目標(biāo)性狀存在極顯著關(guān)聯(lián), 當(dāng)標(biāo)記在兩個(gè)及以上環(huán)境中同時(shí)被檢測(cè)到那么認(rèn)為其是目標(biāo)性狀相對(duì) 穩(wěn)定的關(guān)聯(lián)位點(diǎn).2 .結(jié)果與分析比容與質(zhì)構(gòu)性狀表型變異分析四個(gè)環(huán)境下,小麥粉饅頭比容與質(zhì)構(gòu)表型數(shù)據(jù)如表 2所示.各性 狀均有較大的變異系數(shù),表 2中,E4環(huán)境下饅頭比容性狀的變異系 數(shù)最大為,E1環(huán)境下變異系數(shù)最小衿

15、；表3中,E1環(huán)境黏著 性變異系數(shù)最大% ,彈性變異系數(shù)最小衿.除個(gè)別環(huán)境外,各 性狀的偏度和峰度的絕對(duì)值大局部都小于1,符合正態(tài)分布,變現(xiàn)為數(shù)量性狀遺傳,適合進(jìn)行關(guān)聯(lián)分析.表2四個(gè)環(huán)境下饅頭比容、質(zhì)構(gòu)在群體中的表型數(shù)據(jù)性狀環(huán)境 最小值 最大值 范圍 均值土標(biāo)準(zhǔn)差CV/%偏度峰度比容E1士E2土E3土硬度E1+E2+E3+E4+黏著性E1+E2+E3+E4+彈性E1+E2+E3+E4+黏聚性E1+E2+E3+E4+膠著性E1+咀嚼性回復(fù)性E3E4E1E2E3E4E14943E2E3E4注：E1: 2021年泰安點(diǎn)；E2: 2021年德州點(diǎn)；E3: 2021年泰安點(diǎn)；E4: 2021年德州點(diǎn),余

16、同.SNP標(biāo)記與饅頭比容、質(zhì)構(gòu)相關(guān)性狀的關(guān)聯(lián)分析通過(guò)對(duì)四個(gè)環(huán)境中小麥粉饅頭性狀與標(biāo)記間的關(guān)聯(lián)分析,共得到42個(gè)比容性狀顯著關(guān)聯(lián)位點(diǎn)代,分布于小麥21條染色體中的16 條,單個(gè)位點(diǎn)表型遺傳變異奉獻(xiàn)率為 其中8個(gè)極顯著關(guān)聯(lián)位點(diǎn) 代1,同時(shí)也是高遺傳奉獻(xiàn)率位點(diǎn)F2>10% , 2個(gè)相對(duì)穩(wěn)定位 點(diǎn)在兩個(gè)及以上環(huán)境中表達(dá),分布于小麥的2A、2B、2D 3A、4B、6B、7A染色體上.位于4B染色體上的極顯著關(guān)聯(lián)位點(diǎn) Tdurum_contig4974_355遺傳奉獻(xiàn)率最大,可解釋 %勺表型變異,但只在E4環(huán)境中檢測(cè)到表3四個(gè)環(huán)境下共檢測(cè)到313個(gè)質(zhì)構(gòu)性狀顯著關(guān)聯(lián)位點(diǎn),分布于小麥 的17條染色體上,

17、單個(gè)位點(diǎn)表型變異奉獻(xiàn)率為 其中31個(gè)極顯 著代1 關(guān)聯(lián)位點(diǎn),11個(gè)相對(duì)穩(wěn)定關(guān)聯(lián)位點(diǎn),46個(gè)高遺傳奉獻(xiàn)率 位點(diǎn),分布于小麥的15條染色體上1A、1B、2A 2B 2n 3A、3B 4A、5A 5B、5D 6A、7A 7B和7.同時(shí),檢測(cè)到 5個(gè)極顯著位 點(diǎn),如3B染色體上黏聚性關(guān)聯(lián)位點(diǎn) Kukri_c13329_80O> 7B染色體上 咀嚼性關(guān)聯(lián)位點(diǎn) Tdurum_contig61884_836等,在兩個(gè)環(huán)境中表達(dá), 且奉獻(xiàn)率大于10%為主效關(guān)聯(lián)位點(diǎn).表3四個(gè)環(huán)境中與饅頭比容、質(zhì)構(gòu)性狀相關(guān)的極顯著 A 1、高奉獻(xiàn)率和穩(wěn)定位點(diǎn)標(biāo)記染色體位置R/%P值環(huán)境比容BobWhite_c31163_6

18、942A143E1Kukri_c58096_4802B134,E1,E4Kukri_c13329_8002D37E4GENE-1820_6613A91E1Ku_c73010_1433A91E1Excalibur_c41557_1473A89E1Tdurum_contig4974_3554B61E46B24E17A42E4tplb0027d 07_6337A60,E1,E4黏著性Kukri_c59535_1861B161E3Kukri_c79633_882A163,E1,E2Kukri_c102346_6682A48E4GENE-0592_2682B57E3RAC875_rep_c107702_

19、752B161E2Kukri_c19434_9362D9E4BS00022276_512D18E3Kukri_c1526_6662D97E2BS00110564_513A129E2RFL_Contig5418_3473B70E33B70,E2,E3RAC875_c58159_9893B71E3Tdurum_contig23273_3155B111,E3,E4GENE-2794_5345B110E3BS00084907_515B144E3BS00067911_517A232E47B136E4BS00023069_517B171E2咀嚼性Excalibur_c4948_907B145E2Tduru

20、m_contig61884_8367B148,E1,E2IAAV88367B144E2BS00041585_512B70E1黏聚性BS00065168_511A17E2Kukri_c13329_8002D37,E1,E4Tdurum_contig5009_3493A182E2RFL_Contig3008_13703B9E3Tdurum_contig45817_1933B106E1BS00067744_515B101,E3,E4RAC875_c27696_7187A136E2Tdurum_contig56175_7917A136E2硬度BS00041585_512B70E1IAAV42062B7

21、0E1RAC875_c12766_4612B70E1IAAV22772B70E1BobWhite_c8436_3914A153,E1,E4Tdurum_contig61884_8367B148E2Excalibur_c4948_907B145E2IAAV88367B144E2BS00066342_517B155,E2,E3彈性1A71E3Ex_c21450_3961A71E3Ra_c69908_18771A71E3Ex_c3201_10461A140E22A83E2IAAV15352B145E2Tdurum_contig10048_612B146E2Tdurum_contig52627_726

22、2B146E2BobWhite_c12911_7882B147E2wsnp_CAP11_c3226_15880702B147E2Excalibur_c4964_2755A39E2BS00099401_516A141E2GENE-4717_7967D193E2回復(fù)性Kukri_c13329_8002D37E1RAC875_c5427_4473B92E2RAC875_c27696_7187A136,E2,E4膠著性Ex_c5445_9815A16,E1,E2BS00000020_515D103,E1,E23.討論標(biāo)記本身的特性決定了其在遺傳連鎖圖譜上的分布密度,進(jìn)而對(duì)其所定位的QTL產(chǎn)生影響,本研

23、究整合的遺傳連鎖圖譜全長(zhǎng) 3 cM, 標(biāo)記間平均距離cM,且標(biāo)記的數(shù)量遠(yuǎn)超過(guò)4 000個(gè).因此,該圖譜 具有分子標(biāo)記數(shù)目較多,覆蓋的遺傳距離長(zhǎng),標(biāo)記間平均距離小等突 出特點(diǎn),且該圖譜的建成將有助于鑒別和挖掘優(yōu)異的遺傳變異位點(diǎn). 在所有的標(biāo)記中,B染色體組檢測(cè)到的標(biāo)記數(shù)目最多,A染色體組次 之,D染色體組標(biāo)記數(shù)目最少,這可能是由于小麥 D染色體組具有相 對(duì)較高的保守性造成的閩.本研究利用SNP標(biāo)記對(duì)饅頭比容和質(zhì)構(gòu)相關(guān)性狀進(jìn)行關(guān)聯(lián)分析,采用MLM莫型,將協(xié)變量每個(gè)品種個(gè)體的 Q值、親緣關(guān)系納入回 歸分析,并設(shè)置較高的閾值PW 1 來(lái)預(yù)防因親緣關(guān)系和群體分層 所引發(fā)的偽關(guān)聯(lián),從而保證實(shí)驗(yàn)結(jié)果的可信度

24、.在不同環(huán)境中所得到 的位點(diǎn)常會(huì)出現(xiàn)不一致的情況,或許是由于環(huán)境的作用,這是多基因 限制的數(shù)量性狀的首要特點(diǎn).有些位點(diǎn)在兩個(gè)及以上環(huán)境中同時(shí)被檢 測(cè)到,被稱作相對(duì)穩(wěn)定的關(guān)聯(lián)位點(diǎn).與 SSFfe記相比,SNPfe記與功 能基因的關(guān)聯(lián)更加緊密,這是由于SNPfe記不僅在小麥基因中有遺傳 穩(wěn)定、數(shù)量多等特點(diǎn),而且有些基因內(nèi)的SN哈對(duì)蛋白質(zhì)的結(jié)構(gòu)和表 達(dá)有直接影響27.本研究通過(guò)關(guān)聯(lián)分析得到2個(gè)比容性狀相對(duì)穩(wěn)定位 點(diǎn),11個(gè)質(zhì)構(gòu)性狀相對(duì)穩(wěn)定位點(diǎn),如 E1、E4環(huán)境中同時(shí)檢測(cè)到的與 比容顯著關(guān)聯(lián)的位點(diǎn)tplb0027d07_633, E1、E4個(gè)環(huán)境中檢測(cè)到的與 硬度關(guān)聯(lián)的位點(diǎn)BobWMte_c8436

25、_39侍,可作為參考應(yīng)用于小麥分 子標(biāo)記輔助育種.4.結(jié)論利用分布于小麥全基因組的24 355個(gè)SNP&點(diǎn)對(duì)205份不同小 麥粉饅頭的比容和質(zhì)構(gòu)性狀進(jìn)行全基因組關(guān)聯(lián)分析.檢測(cè)到42個(gè)饅頭比容性狀顯著關(guān)聯(lián)位點(diǎn),其中8個(gè)極顯著P< 1且高遺傳奉獻(xiàn)位 點(diǎn),2個(gè)相對(duì)穩(wěn)定關(guān)聯(lián)位點(diǎn),分布于小麥的7條染色體上.檢測(cè)到313 個(gè)饅頭質(zhì)構(gòu)性狀顯著關(guān)聯(lián)位點(diǎn),有 31個(gè)極顯著代1 關(guān)聯(lián)位點(diǎn), 11個(gè)相對(duì)穩(wěn)定關(guān)聯(lián)位點(diǎn),46個(gè)高遺傳奉獻(xiàn)率位點(diǎn)R2>10%,分布 于小麥的15條染色體上.同時(shí),檢測(cè)到5個(gè)質(zhì)構(gòu)性狀主效關(guān)聯(lián)位點(diǎn). 本實(shí)驗(yàn)所得到的這些標(biāo)記對(duì)從分子水平深入研究小麥粉的品質(zhì)性狀 具有重要意義,并

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