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作物学报

作物学报 ›› 2025, Vol. 51 ›› Issue (3): 568-585.doi: 10.3724/SP.J.1006.2025.44051

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

中国高粱株高和节间数全基因组关联分析及候选基因预测

徐建霞(), 丁延庆(), 曹宁, 程斌, 高旭, 李文贞, 张立异()   

  1. 贵州省农业科学院旱粮研究所, 贵州贵阳 550006
  • 收稿日期:2024-03-19 接受日期:2024-10-25 出版日期:2025-03-12 网络出版日期:2024-11-28
  • 通讯作者: *张立异, E-mail: lyzhang1997@hotmail.com
  • 作者简介:徐建霞, E-mail: 529438648 @qq.com;
    丁延庆, E-mail: dyqcyl@163.com

    **同等贡献

  • 基金资助:
    贵州省基础研究计划(自然科学)项目(QKH Foundation-[2024] Youth 077);贵州省科技计划项目(QKH Foundation-ZK [2023] General 169);贵州省科技计划项目(QKH Foundation-ZK [2022] General 235);国家自然科学基金项目(32160459);贵州省育种科研基础平台创新能力建设项目(QKH Enterprise Service[2022] 014);科研机构创新能力建设项目(QKH Enterprise Service[2022] 007);贵州省农科院项目(QNK Germplasm Resources[2023] 06)

Genome-wide association analysis and prediction of candidate genes for plant height and internode number in Chinese sorghum

XU Jian-Xia(), DING Yan-Qing(), CAO Ning, CHENG Bin, GAO Xu, LI Wen-Zhen, ZHANG Li-Yi()   

  1. Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
  • Received:2024-03-19 Accepted:2024-10-25 Published:2025-03-12 Published online:2024-11-28
  • Contact: *E-mail: lyzhang1997@hotmail.com
  • About author:

    **Contributed equally to this work

  • Supported by:
    Guizhou Provincial Basic Research Program (Natural Science)(QKH Foundation-[2024] Youth 077);Guizhou Provincial Science and Technology Program Project(QKH Foundation-ZK [2023] General 169);Guizhou Provincial Science and Technology Program Project(QKH Foundation-ZK [2022] General 235);National Natural Science Foundation of China(32160459);Innovation Capacity Building Project for Breeding Research Platforms in Guizhou Province(QKH Enterprise Service[2022] 014);Innovation Capacity Building Project for Research Institutions(QKH Enterprise Service[2022] 007);Guizhou Academy of Agricultural Sciences Project(QNK Germplasm Resources[2023] 06)

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摘要：

适当降低株高可以提高植物的养分利用效率和抗倒伏性, 对高粱的高产和稳产具有重要意义。为揭示高粱株高遗传机制, 本研究以242份中国高粱为研究对象, 利用2,015,850个单核苷酸多态性(SNP)标记, 在7个不同环境条件下对株高、节间数及节间长度进行全基因组关联分析(Genome-wide association study, GWAS)。表型调查表明, 株高、节间数和节间长度的表型变异系数在13.47%~30.06%之间, 在所有环境下的偏度和峰度的绝对值均小于1。利用2种不同的关联模型(Blink和FarmCPU)对株高、节间数及节间长度进行GWAS分析, 在10条染色体上共鉴定出118个与这3个性状显著相关的数量性状核苷酸(QTN)。其中, 与株高、节间数及节间长度显著相关的QTN分别为60个、37个和32个, 株高与节间数、节间长度共定位QTN分别有8个和3个。通过对候选基因的序列分析和功能注释, 在12个QTN置信区间或附近鉴定出14个候选基因, 它们与水稻和玉米中参与糖代谢、激素合成与信号传递以及细胞分裂的基因同源。选择性消除分析揭示, 位于1号染色体的候选基因Sobic.001G510400在中国南北高粱群体中受到强烈选择, 形成了以北方矮秆高粱为主的单倍型Hap1和以南方高秆高粱为主的单倍型Hap2。携有Hap1的北方种质871255和携有Hap2的南方种质红缨子之间, 该基因表达存在显著差异。本研究结果为中国高粱品种株高遗传改良提供了理论依据。

关键词: 高粱, 株高, 节间数, 全基因组关联分析(GWAS), 候选基因

Abstract:

An appropriate reduction in plant height is essential for improving nutrient utilization efficiency and lodging resistance, both of which significantly contribute to achieving high and stable yields. This study investigated 242 Chinese sorghum accessions to elucidate the genetic mechanisms underlying plant height. A genome-wide association study (GWAS) was performed using 2,015,850 single nucleotide polymorphisms (SNPs) to analyze plant height, internode number, and internode length across seven environments. The results showed that the phenotypic variation coefficients for plant height, internode number, and internode length ranged from 13.47% to 30.06%, with absolute skewness and kurtosis values less than 1 under all conditions. Using two association models (Blink and FarmCPU), the GWAS identified 118 quantitative trait nucleotides (QTNs) significantly associated with the three traits across 10 chromosomes. Specifically, 60, 37, and 32 QTNs were significantly associated with plant height, internode number, and internode length, respectively. Eight QTNs were co-located for both plant height and internode number, while three QTNs were co-located for internode length. Through sequence analysis and functional annotation of candidate genes, 14 genes related to plant height and internode number were identified within or near the confidence intervals of 12 QTNs. These genes were homologous to those involved in sugar metabolism, hormone synthesis and signaling, and cell division in rice and maize. Selective sweep analysis revealed strong selection pressure on the candidate gene Sobic.001G510400 on chromosome 1 in Chinese sorghum populations, resulting in the formation of Hap1, which is dominant in northern dwarf sorghum, and Hap2, which is dominant in southern tall sorghum. Significant expression differences of this gene were observed between the northern accession 871255 (Hap1) and the southern accession Hongyingzi (Hap2). These findings provide a theoretical foundation for the genetic improvement of plant height in Chinese sorghum varieties.

Key words: sorghum, plant height, internode number, genome-wide association analysis, GWAS, candidate genes

表1

供试材料来源及份数"

来源地
Originated location		 材料份数
Number of materials		 来源地
Originated location		 材料份数
Number of materials
辽宁Liaoning 39 吉林Jilin 5
山西Shanxi 28 贵州Guizhou 37
内蒙古Inner Mongolia 17 云南Yunnan 21
陕西Shaanxi 17 四川Sichuan 19
山东Shandong 12 湖北Hubei 10
河北Hebei 12 安徽Anhui 3
北京Beijing 11 广西Guangxi 2
黑龙江Heilongjiang 8 江苏Jiangsu 1

表2

株高、节间数和节间长度表型统计分析"

性状
Trait		 环境
Environment		 最小值
Min.		 最大值
Max.		 平均值
Mean		 标准差
SD		 变异系数
CV (%)		 偏度
Skewness		 峰度
Kurtosis
株高
PH		 2018贵阳 2018GY 104.60 342.10 219.04 50.93 23.25 0.07 -0.46
2019贵阳 2019GY 98.67 346.33 220.02 49.95 22.70 0.02 -0.41
2019杭州 2019HZ 110.80 437.63 263.27 69.22 26.29 0.18 -0.38
2019陵水 2019LS 104.33 316.00 195.05 39.77 20.39 0.41 0.14
2020贵阳 2020GY 110.43 439.33 279.04 66.53 23.84 -0.25 -0.22
2020乐东 2020LD 109.13 280.50 186.82 32.35 17.32 0.19 0.09
2021贵阳 2021GY 128.50 375.33 244.60 52.89 21.63 -0.05 -0.35
节间数IN 2018贵阳 2018GY 3.80 10.50 6.58 1.45 21.99 0.35 -0.50
2019贵阳 2019GY 3.00 11.75 6.54 1.56 23.92 0.28 -0.02
2019杭州 2019HZ 4.00 15.33 9.00 2.70 30.06 0.45 -0.26
2019陵水 2019LS 4.33 11.00 7.01 1.09 15.57 0.33 0.69
2020贵阳 2020GY 5.14 13.33 9.04 1.38 15.26 -0.24 0.14
2020乐东 2020LD 3.50 9.63 6.46 1.07 16.56 0.12 0.32
2021贵阳 2021GY 4.80 12.75 7.90 1.40 17.74 0.49 0.98
节间
长度
IL		 2018贵阳 2018GY 19.62 49.72 33.68 6.10 18.11 -0.02 -0.52
2019贵阳 2019GY 17.88 50.92 33.95 7.77 22.89 0.25 -0.53
2019杭州 2019HZ 17.92 50.60 30.34 4.62 15.24 0.88 2.31
2019陵水 2019LS 17.60 45.88 27.93 4.83 17.31 0.62 0.50
2020贵阳 2020GY 13.14 47.13 30.77 5.76 18.73 -0.16 0.04
2020乐东 2020LD 18.12 40.33 29.10 3.92 13.47 0.02 -0.23
2021贵阳 2021GY 14.26 42.54 31.14 5.38 17.29 -0.36 -0.11

图1

株高、节间数和节间长度频数分布图 云雨图表示不同环境株高(图1-A)、节间数(图1-B)和节间长度(图1-C)频数分布情况, 黄色、浅蓝色、绿色、紫色、浅黄色、浅紫色、浅绿色分别表示2018年贵阳、2019年贵阳、2020年贵阳、2021贵阳、2019年杭州、2019年陵水和2020年乐东环境下的表型。"

图2

7个环境下株高、节间数和节间长度相关性分析 **表示在0.01水平显著相关; *表示在0.05水平显著相关。不同环境下的表型采用“年份+地点_性状”来表示。18、19、20和21分别代表2018、2019、2020和2021年; GY、HZ、LS和LD分别表示贵阳、杭州、陵水和乐东; PH、IN和 IL分别表示株高、节间数和节间长度。"

表3

株高、节间数和节间长度间方差分析及广义遗传力"

性状
Trait		 均方 Mean square 方差Variance F值 F-value 广义遗传力Broad-sense heritability
基因型
Genotype		 环境
Environment		 基因型
×环境
G×E		 基因型
Genotype		 环境
Environment		 基因型
×环境
G×E		 基因型
Genotype		 环境
Environment		 基因型
×环境
G×E
株高 PH 46,407.51 813,299.34 1867.31 2248.60 1155.41 551.77 196.32** 3440.49** 7.89** 0.90
节间数 IN 30.45 868.82 4.00 1.33 1.26 1.17 58.64** 1673.40** 7.71** 0.79
节间长度 IL 483.50 25,339.99 97.47 19.52 36.89 19.47 12.02** 629.91** 2.42** 0.71

表4

不同环境下株高、节间数和节间长度显著关联位点汇总"

数量性状
核苷酸
QTN		 染色体
Chr.		 位置
Position		 次等等位基因频率
MAF		 效应值
Effect		 -log10(P)-
value		 性状
Trait		 环境+模型
Environment + Model
QTN1.2405118 Chr.01 2,405,118 0.29 -0.27 8.62 IN 2018GY (FarmCPU)
QTN1.2551955 Chr.01 2,551,955 0.49 -0.14 7.90 IN BLUP (FarmCPU)
QTN1.4569288 Chr.01 4,569,288 0.02 -1.36 15.28 IN 2019HZ (FarmCPU)
QTN1.5144542 Chr.01 5,144,542 0.30 12.59 8.33 PH 2020GY (FarmCPU)
QTN1.5629263 Chr.01 5,629,263 0.20 10.10 8.22 PH BLUP (FarmCPU)
QTN1.7184266 Chr.01 7,184,266 0.01 1.86 9.32 IN 2019LS (FarmCPU), 2021GY (Blink, FarmCPU)
QTN1.19414155 Chr.01 19,414,155 0.25 1.64 8.20 IL 2021GY (FarmCPU)
QTN1.23001725 Chr.01 23,001,725 0.01 2.16 7.36 IN 2019LS (FarmCPU)
QTN1.52105747 Chr.01 52,105,747 0.01 -39.48 7.42 PH 2018GY (FarmCPU)
QTN1.57894341 Chr.01 57,894,341 0.23 0.55 18.60 IN 2021GY (FarmCPU)
QTN1.73232722 Chr.01 73,232,722 0.08 17.86 8.08 PH BLUP (FarmCPU)
QTN1.75754022 Chr.01 75,754,022 0.02 NA 9.10 PH 2019HZ (Blink)
QTN1.75986905 Chr.01 75,986,905 0.18 8.14 8.77 PH 2020LD (FarmCPU)
QTN1.77964551 Chr.01 77,964,551 0.48 NA 11.19 PH 2019GY (Blink), 2020GY (FarmCPU), 2021GY (Blink, FarmCPU)
QTN2.5369719 Chr.02 5,369,719 0.38 -10.54 8.52 PH 2018GY (FarmCPU)
QTN2.5571151 Chr.02 5,571,151 0.45 11.61 13.47 PH BLUP (FarmCPU, Blink)
QTN2.10544191 Chr.02 10,544,191 0.08 NA 7.72 IL 2019HZ (Blink)
QTN2.36051465 Chr.02 36,051,465 0.11 -1.98 7.83 IL 2021GY (FarmCPU)
QTN2.61222038 Chr.02 61,222,038 0.15 0.45 13.64 IN 2018GY (FarmCPU), 2020LD (FarmCPU)
PH 2019HZ (Blink), 2020LD (FarmCPU), BLUP (FarmCPU)
QTN2.61553618 Chr.02 61,553,618 0.07 0.59 9.66 IN 2020GY (FarmCPU), 2021GY (FarmCPU)
QTN2.71720401 Chr.02 71,720,401 0.05 NA 7.22 PH 2019HZ (Blink)
QTN3.3169459 Chr.03 3,169,459 0.06 -27.36 12.20 PH 2018GY (Blink, FarmCPU)
QTN3.3838811 Chr.03 3,838,811 0.04 3.35 7.39 IL 2020GY (FarmCPU)
QTN3.9730138 Chr.03 9,730,138 0.17 -1.64 6.77 IL 2021GY (FarmCPU)
QTN3.27015392 Chr.03 27,015,392 0.01 41.33 6.75 PH 2021GY (FarmCPU)
QTN3.36482112 Chr.03 36,482,112 0.08 -26.89 8.80 PH 202119 (FarmCPU)
QTN3.47562291 Chr.03 47,562,291 0.05 NA 6.69 PH 2019GY (Blink)
QTN3.51305296 Chr.03 51,305,296 0.02 -45.60 7.36 PH 2020GY (FarmCPU)
QTN3.52695022 Chr.03 52,695,022 0.17 NA 8.14 IN BLUP(Blink)
QTN3.53396433 Chr.03 53,396,433 0.18 NA 13.06 IN 2020GY (Blink, FarmCPU)
QTN3.53699753 Chr.03 53,699,753 0.15 0.78 14.87 PH 2019GY(FarmCPU)
IN 2019HZ (FarmCPU)
QTN3.66783610 Chr.03 66,783,610 0.25 0.31 7.84 IN 2020LD (FarmCPU)
QTN3.67461402 Chr.03 67,461,402 0.03 2.74 11.86 IN 2019GY (FarmCPU)
QTN3.69982563 Chr.03 69,982,563 0.07 0.52 18.31 IN BLUP (Blink, FarmCPU)
QTN3.71309333 Chr.03 71,309,333 0.44 0.69 9.21 IL BLUP (FarmCPU)
QTN3.72489056 Chr.03 72,489,056 0.03 NA 8.78 IL 2020LD
QTN3.72974611 Chr.03 72,974,611 0.24 NA 7.06 PH 2019GY (Blink)
QTN4.21358166 Chr.04 21,358,166 0.03 -7.55 6.91 IL 2021GY (FarmCPU)
QTN4.24740647 Chr.04 24,740,647 0.03 -7.58 6.94 IL 2020GY (FarmCPU)
QTN4.39744627 Chr.04 39,744,627 0.06 -3.06 10.06 IL 2019LS (Blink), 2019LS (FarmCPU), 2021GY (FarmCPU)
QTN4.51304388 Chr.04 51,304,388 0.19 -16.98 9.16 PH 2019GY (FarmCPU)
QTN4.56405572 Chr.04 56,405,572 0.44 0.17 6.87 IN 2020LD (FarmCPU)
QTN4.57121231 Chr.04 57,121,231 0.15 -1.48 9.36 IL 2021GY (FarmCPU)
PH 2019LS (Blink)
QTN4.62261029 Chr.04 62,261,029 0.50 1.22 9.06 IL 2020GY (FarmCPU)
QTN4.63570248 Chr.04 63,570,248 0.04 -0.36 7.12 IN BLUP (FarmCPU)
QTN4.65266850 Chr.04 65,266,850 0.43 11.00 12.76 PH 2018GY (FarmCPU)
IL 2020LD (FarmCPU), BLUP (FarmCPU)
QTN4.65863171 Chr.04 65,863,171 0.4 14.04 13.22 IN BLUP (FarmCPU)
PH 2020GY (Blink, FarmCPU), 2021GY (FarmCPU), BLUP (FarmCPU)
QTN5.225941 Chr.05 225,941 0.06 -29.88 9.55 PH 2018GY (FarmCPU)
QTN5.17438732 Chr.05 17,438,732 0.06 2.29 7.77 IL 2021GY (FarmCPU)
QTN5.20666756 Chr.05 20,666,756 0.01 78.55 9.92 PH 2019GY (FarmCPU)
QTN5.35025393 Chr.05 35,025,393 0.15 1.66 7.36 IL 2021GY (FarmCPU)
QTN5.61015103 Chr.05 61,015,103 0.24 -16.48 7.93 PH 2021GY (FarmCPU)
QTN5.65444056 Chr.05 65,444,056 0.01 -56.28 7.83 PH 2018GY (FarmCPU)
QTN5.70860912 Chr.05 70,860,912 0.25 -18.44 11.54 PH 2018GY (FarmCPU), 2019GY (FarmCPU), 2021GY (FarmCPU)
IN 2018GY (FarmCPU)
QTN6.6070840 Chr.06 6,070,840 0.01 1.54 7.26 IN 2019HZ (FarmCPU)
QTN6.6720303 Chr.06 6,720,303 0.05 -3.41 8.91 IL 2020GY (FarmCPU)
QTN6.11512672 Chr.06 11,512,672 0.08 -21.11 9.44 PH 2018GY (FarmCPU)
QTN6.14112048 Chr.06 14,112,048 0.03 NA 9.66 IL 2021GY (Blink)
QTN6.17354113 Chr.06 17,354,113 0.10 -0.89 12.69 IN 2019HZ (FarmCPU)
QTN6.19368812 Chr.06 19,368,812 0.03 0.47 7.00 IN BLUP (FarmCPU)
QTN6.20384517 Chr.06 20,384,517 0.04 3.43 8.71 IL 2020GY (FarmCPU,Blink)
QTN6.21804125 Chr.06 21,804,125 0.12 -0.52 8.37 IN 2019HZ (FarmCPU)
QTN6.30195457 Chr.06 30,195,457 0.01 NA 10.43 IN 2018GY (Blink)
QTN6.39969911 Chr.06 39,969,911 0.31 NA 7.65 IN 2018GY (Blink)
QTN6.47858747 Chr.06 47,858,747 0.17 NA 7.38 PH BLUP (Blink)
QTN6.51781734 Chr.06 51,781,734 0.34 1.58 10.43 IL 2021GY (FarmCPU)
QTN6.58083889 Chr.06 58,083,889 0.07 2.31 7.53 IL 2021GY (FarmCPU)
QTN7.1772505 Chr.07 1,772,505 0.31 1.09 7.83 IL 2021GY (FarmCPU)
QTN7.2186032 Chr.07 2,186,032 0.07 NA 9.09 PH 2019LS (Blink)
QTN7.26630649 Chr.07 26,630,649 0.01 54.39 17.39 PH 2020LD (Blink, FarmCPU)
QTN7.42714173 Chr.07 42,714,173 0.15 -1.03 8.73 IL BLUP (FarmCPU)
PH 2018GY (FarmCPU)
QTN7.49687684 Chr.07 49,687,684 0.09 NA 8.32 IL 2019HZ (FarmCPU, Blink)
QTN7.55183398 Chr.07 55,183,398 0.04 -3.34 6.92 IL 2020GY (FarmCPU)
QTN7.56139617 Chr.07 56,139,617 0.01 NA 10.10 IN 2019HZ (Blink, FarmCPU)
QTN7.58438538 Chr.07 58,438,538 0.34 0.51 10.74 IN 2018GY (FarmCPU)
QTN7.59393707 Chr.07 59,393,707 0.02 NA 12.03 PH BLUP (Blink)
QTN7.59653890 Chr.07 59,653,890 0.20 NA 10.82 PH 2019LS (Blink), 2020LD (FarmCPU)
QTN7.59721216 Chr.07 59,721,216 0.15 21.54 7.48 PH 2019GY (FarmCPU), 2020GY (FarmCPU), BLUP (FarmCPU)
QTN7.60501279 Chr.07 60,501,279 0.04 26.10 10.81 PH 2018GY (Blink, FarmCPU)
QTN7.60940816 Chr.07 60,940,816 0.10 -1.92 8.70 IL 2020GY (FarmCPU)
QTN7.62144455 Chr.07 62,144,455 0.06 -4.42 14.15 IL 2021GY (FarmCPU)
QTN8.2105446 Chr.08 2,105,446 0.11 -18.15 8.47 PH BLUP (FarmCPU)
QTN8.4977795 Chr.08 4,977,795 0.07 27.21 11.93 PH 2018GY (FarmCPU), 2019HZ (Blink), 2021GY (FarmCPU)
QTN08.8249188 Chr.08 8,249,188 0.34 13.21 9.24 PH BLUP (FarmCPU)
QTN8.8955240 Chr.08 8,955,240 0.01 72.34 11.00 PH 2020GY (FarmCPU)
QTN8.13232192 Chr.08 13,232,192 0.04 -97.42 7.04 PH 2020GY (FarmCPU)
QTN8.13747177 Chr.08 13,747,177 0.12 -17.00 10.04 PH 2020LD (FarmCPU)
QTN8.18073491 Chr.08 18,073,491 0.18 0.36 8.72 IN 2020LD (FarmCPU)
QTN8.46279959 Chr.08 46,279,959 0.24 15.75 6.66 PH 2021GY (FarmCPU)
QTN8.50392737 Chr.08 50,392,737 0.41 10.55 10.18 PH 2018GY (FarmCPU)
QTN8.57976551 Chr.08 57,976,551 0.38 6.20 8.01 PH 2020LD (FarmCPU)
IN BLUP (Blink)
QTN8.59708198 Chr.08 59,708,198 0.46 22.46 20.80 PH 2019GY (Blink, FarmCPU), 2020GY (Blink, FarmCPU), 2021GY (FarmCPU), BLUP (FarmCPU)
IN 2018GY (FarmCPU), 2019GY (Blink), 2019HZ (FarmCPU), 2020GY (FarmCPU), 2021GY
(FarmCPU), BLUP (FarmCPU)
QTN8.60514221 Chr.08 60,514,221 0.04 4.24 11.16 IL 2021GY (FarmCPU)
QTN8.61141049 Chr.08 61,141,049 0.10 NA 6.72 PH 2020LD (Blink)
QTN9.9011331 Chr.09 9,011,331 0.04 NA 8.04 IL 2021GY (Blink)
QTN9.9723995 Chr.09 9,723,995 0.02 -1.26 9.13 IN 2020GY (FarmCPU)
QTN9.13457659 Chr.09 13,457,659 0.02 -2.20 7.58 IL BLUP (FarmCPU)
QTN9.14023575 Chr.09 14,023,575 0.04 -6.79 7.28 IL 2019GY (FarmCPU)
QTN9.16091197 Chr.09 16,091,197 0.03 4.48 6.90 IN 2019HZ (Blink)
QTN9.21770577 Chr.09 21,770,577 0.04 21.71 6.75 PH BLUP (FarmCPU)
QTN9.24272625 Chr.09 24,272,625 0.03 -92.74 7.08 IN 2019LS (FarmCPU)
QTN9.26282863 Chr.09 26,282,863 0.12 -21.59 7.89 PH 2019GY (FarmCPU)
QTN9.40913786 Chr.09 40,913,786 0.06 NA 9.21 PH 2019HZ (Blink)
QTN9.45916233 Chr.09 45,916,233 0.06 2.86 7.86 IL 2020GY (FarmCPU)
QTN9.51292519 Chr.09 51,292,519 0.01 -63.41 7.17 PH 2019GY (FarmCPU)
QTN9.53210328 Chr.09 53,210,328 0.05 31.32 6.94 PH 2020GY (FarmCPU)
QTN9.59349793 Chr.09 59,349,793 0.49 2.91 9.54 IL 2020GY (FarmCPU), BLUP (FarmCPU, Blink)
QTN10.1694341 Chr.10 1,694,341 0.19 0.96 14.00 IN 2019GY (FarmCPU)
PH 2018GY (Blink, FarmCPU)
QTN10.3945045 Chr.10 3,945,045 0.07 NA 8.06 IN BLUP (Blink)
QTN10.12448273 Chr.10 12,448,273 0.11 -0.53 10.57 PH 2019GY (FarmCPU)
IN 2020GY (Blink, FarmCPU), 2021GY (Blink), BLUP (FarmCPU)
QTN10.12598609 Chr.10 12,598,609 0.15 16.40 10.00 PH 2020GY (FarmCPU, Blink)
QTN10.13745644 Chr.10 13,745,644 0.01 52.08 8.78 PH 2018GY (FarmCPU)
QTN10.19774145 Chr.10 19,774,145 0.02 41.69 9.73 PH 2018GY (FarmCPU)
QTN10.26748555 Chr.10 26,748,555 0.02 47.76 8.41 PH 2020GY (FarmCPU)
QTN10.34601077 Chr.10 34,601,077 0.04 0.33 7.74 IN BLUP (FarmCPU)
QTN10.55997217 Chr.10 55,997,217 0.45 -0.16 9.49 IN BLUP (FarmCPU)
QTN10.57784636 Chr.10 57,784,636 0.04 29.25 7.78 PH 2019GY (FarmCPU)
QTN10.60576093 Chr.10 60,576,093 0.01 31.62 6.62 PH 2020LD (FarmCPU)

附图1-A

株高在Blink (a)和FarmCPU (b) 2种模型下的 Manhattan图及QQ-plot图 环境处理缩写同表2。"

附图1-B

节间数在Blink (a)和FarmCPU (b) 2种模型下的 Manhattan图及QQ-plot图 环境处理缩写同表2。"

附图1-C

节间长度在Blink (a)和FarmCPU (b) 2种模型下的Manhattan图及QQ-plot图 环境处理缩写同表2。"

表5

重要QTN区间候选基因功能注释"

QTN 候选基因
Candidate gene		 基因组位置
Genomic location		 同源基因
Orthologous gene		 基因名称
Gene name		 蛋白注释
Proteins annotation		 相似性
Similarity (%)

QTN1.4569288		 Sobic.001G060100 Chr01:4502760−4511929 LOC_Os03g57940 CKI 酪蛋白激酶;抽穗期基因Casein kinase; heading stage gene 89
Sobic.001G062900 Chr01:4700933−4706989 Zm00001d034383 VP8 调控分生组织发育 Regulate meristem development 95
QTN1.57894341 Sobic.001G298400 Chr01:57918398−57922897 LOC_Os07g15770 Ghd7 每穗粒数、株高和抽穗期多效性控制基因; 氮肥利用率Grains, height, and heading date gene; nitrogen utilization efficiency 58
QTN1.77964551 Sobic.001G510400 Chr01:77810869−77813714 LOC_Os03g04680 OsCYP96B4 细胞色素P450; 半矮秆 Cytochrome P450; semi-dwarf 77
QTN2.61222038 Sobic.002G221900 Chr02:61366555−61368022 LOC_Os09g27820 OsACO1 1-氨基环丙烷-1-羧酸氧化酶基因
1-aminocyclopropane-1-carboxylate oxidase gene		 89
QTN3.3838811 Sobic.003G040900 Chr03:3821972−3830666 LOC_Os01g08700 OsGI 生物钟相关Gigantea 95.6
QTN3.67461402 Sobic.003G358400 Chr03:67621227−67632849 Zm00001d042843 NA1 油菜素内酯早期生物合成
Early step in brassinosteroid biosynthesis		 95
QTN3.72974611 Sobic.003G425300 Chr03:72974769−72978763 Zm00001d011876 ELM1 光敏色素合成Photosensitive pigment synthesis 91
Sobic.003G427600 Chr03:73106228−73116438 LOC_Os03g24220 VLN2 绒毛蛋白Villin 94
QTN4.56405572 Sobic.004G214100 Chr04:56389818−56395087 LOC_Os02g40030 OsNST1 核苷酸糖转运蛋白; 脆茎
Oryza sativa nucleotide sugar transport; brittle culm		 96
QTN4.65266850 Sobic.004G317000 Chr04:65266844−65268995 LOC_Os02g53690 OsGRF1 生长调节因子 Growth regulating factor 85
QTN4.65863171 Sobic.004G323600 Chr04:65819834−65821680 LOC_Os02g54600 OsMKK4 丝裂原活化蛋白激酶;小粒
Mitogen activated protein Kinase; small grain		 86
QTN7.59721216 Sobic.007G163800(Dw3) Chr07:59821904−59829921 Zm00001d031871 BR2 生长素极性运输 Polar auxin transport 94
LOC_Os08g45030 SD8 矮秆基因; 三磷酸腺苷结合盒转运体B1
Semi-dwarf; ATP BINDING CASSETTE B1 transporter		 93
QTN9.53210328 Sobic.009G176400 Chr09:53137542−53147354 LOC_Os05g40384 EUI1 长穗颈基因 elongated uppermost internode 88

表6

Tajima’D、Fst和Pi前5%对应值及基因数"

项目
Item		 窗口数
Number of windows		 前5%窗口数
Number of top 5% windows		 前5%对应值
Top 5% of the value		 前5%对应基因数
Top 5% of genes
南方_ Tajima’D
South_ Tajima’D		 60,150 3008 ≤ -1.9081 1903
北方_ Tajima’D
North_ Tajima’D		 60,663 3033 ≤ -1.8004 2834
南方/北方_Pi
South/north_Pi		 59,287 2964 ≥ 7.5425 2674
南方/北方_Fst
South/north_Fst		 61,524 3076 ≥ 0.5384 2478

表7

14个候选基因Tajima’s D、Fst和Pi检测结果"

QTN 候选基因
Candidate gene		 基因组位置
Genomic location		 南方_Tajima’D
South_Tajima’D		 北方_Tajima’D
North_Tajima’D		 南方/北方_Pi
South/north_Pi		 南方/北方_Fst
South/north_Fst
QTN1.4569288 Sobic.001G060100 Chr.01: 4502760-4511929 0.63323 1.17192 0.70587 0.50171
Sobic.001G062900 Chr.01: 4700933-4706989 — — — —
QTN1.57894341 Sobic.001G298400 Chr.01: 57918398-57922897 -0.28265 3.70518 0.44059 0.20719
QTN1.77964551 Sobic.001G510400 Chr.01: 77810869-77813714 4.12955 -1.09660 240.75045 0.42020
QTN2.61222038 Sobic.002G221900 Chr.02: 61366555-61368022 1.63095 -0.83259 0.62484 0.24644
QTN3.3838811 Sobic.003G040900 Chr.03: 3821972-3830666 2.96779 -0.47567 4.26399 0.45506
QTN3.67461402 Sobic.003G358400 Chr.03: 67621227-67632849 -1.33349 2.21191 0.22586 0.12627
QTN3.72974611 Sobic.003G425300 Chr.03: 72974769-72978763 4.87495 -0.75596 3.53964 0.35919
Sobic.003G427600 Chr.03: 73106228-73116438 4.11883 5.32407 0.91151 0.03476
QTN4.56405572 Sobic.004G214100 Chr.04: 56389818-56395087 2.65072 2.36931 0.76241 0.08865
QTN4.65266850 Sobic.004G317000 Chr.04: 65266844-65268995 2.35182 4.79370 0.73469 0.23975
QTN4.65863171 Sobic.004G323600 Chr.04: 65819834-65821680 -0.80385 4.90854 0.29065 0.41327
QTN7.59721216 Sobic.007G163800 Chr.07: 59821904-59829921 1.23952 -1.61676 7.32019 0.25767
QTN9.53210328 Sobic.009G176400 Chr.09: 53137542-53147354 1.69947 -1.47816 17.04476 0.44604

图3

Sobic.001G510400基因在Hap1和Hap2单倍型间外显子的SNP变异"

图4

携有Hap1和Hap2的高粱种质的频率分布"

图5

7个环境下携有Hap1和Hap2高粱种质的株高箱线图 *** 表示在0.001水平显著相关; * 表示在0.05水平显著相关。"

图6

株高候选基因Sobic.001G510400的表达特征 *表示在0.05水平显著相关。"

附表1

本研究定位到的QTN及已报道的QTL"

本研究定位到的QTN
QTN located in this study		 已报道的QTL
QTL reported
QTN 染色体
Chromosome		 SNP 位置
SNP position		 QTL Id 出版
Publication		 群体
Population		 性状
Trait description		 起始-结束
LG:Start-End (v3.0)
QTN1.2405118 Chr01 2405118 QHGHT1.37 Liu et al. 2019 Tx623 x S. virgatum Plant height 1:0-4093151
QTN1.2551955 Chr01 2551955
QTN1.4569288 Chr01 4569288
QTN1.5144542 Chr01 5144542 QHGHT1.2 Kebede et al. 2001 SC56/Tx7000 Height (plant height) 1:4862819-7562505
QTN1.5629263 Chr01 5629263
QTN1.7184266 Chr01 7184266
QTN1.19414155 Chr01 19414155
QTN1.23001725 Chr01 23001725
QTN1.52105747 Chr01 52105747 QHGHT1.5 Hart et al. 2001 BTx623/IS3620C Height (plant height) 1:24186681-52681319
QTN1.57894341 Chr01 57894341 QHGHT1.8 Guan et al. 2011 Shihong137/L-Tian Height (plant height) 1:54541207-58709704
QTN1.73232722 Chr01 73232722 QHGHT1.21 Mocoeur et al. 2015 E-Tian/Ji2731 Height (plant height) 1:69892099-74204679
QTN1.75754022 Chr01 75754022 QHGHT1.17 Wang et al. 2014a IS8525/R931945-2-2 Height (plant height) 1:74818452-78396425
QTN1.75986905 Chr01 75986905
QTN1.77964551 Chr01 77964551 QHGHT1.19 Parh 2005 IS8525/R931945-2-2 Height (plant height) 1:77677015-80878678
QTN2.5369719 Chr02 5369719
QTN2.5571151 Chr02 5571151
QTN2.10544191 Chr02 10544191
QTN2.36051465 Chr02 36051465 QHGHT2.6 Bouchet et al. 2017 Nested Association Mapping set US Height (plant height) 2:20403133-48551270
QTN2.61222038 Chr02 61222038 QHGHT2.13 Liu et al. 2019 Tx623 / S. virgatum Height (plant height) 2:60182134-66050977
QTN2.61553618 Chr02 61553618
QTN2.71720401 Chr02 71720401
QTN3.3169459 Chr03 3169459 QHGHT3.4 Phuong et al. 2013 IS2449/IS1488 Height (plant height) 3:3030648-6095949
QTN3.3838811 Chr03 3838811
QTN3.9730138 Chr03 9730138
QTN3.27015392 Chr03 27015392
QTN3.36482112 Chr03 36482112
QTN3.47562291 Chr03 47562291
QTN3.51305296 Chr03 51305296
QTN3.52695022 Chr03 52695022
QTN3.53396433 Chr03 53396433
QTN3.53699753 Chr03 53699753 qCNN3.1 xu et al. 2023 BTx623/HYZ Internode number 3:53577719—55061159
QTN3.66783610 Chr03 66783610 QHGHT3.18 Bai et al. 2017 BTx623/Rio Height (plant height) 3:65416545-69211928
QTN3.67461402 Chr03 67461402 QHGHT3.18
QHGHT3.20
QHGHT3.24		 Bai et al. 2017
Harris-Shultz et al. 2015
Liu et al. 2019		 BTx623/Rio
HoneyDrip/Collier
Tx623 / S. virgatum		 Height (plant height) 3:65416545-69211928
3:67037126-67647534
3:67111051-72337616
QTN3.69982563 Chr03 69982563 QHGHT3.16 Nagaraja Reddy et al. 2013 M35-1/B35 Height (plant height) 3:69933510-72862046
QTN3.71309333 Chr03 71309333
QTN3.72489056 Chr03 72489056
QTN3.72974611 Chr03 72974611 QHGHT3.16 Nagaraja Reddy et al. 2013 M35-1/B35 Height (plant height) 3:69933510-72862046
QTN4.21358166 Chr04 21358166 QHGHT4.1
QHGHT4.10
 Mocoeur et al. 2015
Klein et al. 2001		 E-Tian/Ji2731
RTx430/Sureno		 Height (plant height)
Height (plant height)		 4:10150746-51097958
4:13362712-50084108
QTN4.24740647 Chr04 24740647
QTN4.39744627 Chr04 39744627
QTN4.51304388 Chr04 51304388

QTN4.56405572
Chr04
56405572		 qCNN4.2
QHGHT4.16
QHGHT4.13		 xu et al. 2023
Mocoeur et al. 2015
Nagaraja Reddy et al. 2013		 BTx623/HYZ
E-Tian/Ji2731
M35-1/B35		 Internode number
Height (plant height)
Height (plant height)		 4:55918714-57111301
4:53628830-61766744
4:55962847-61572196
QTN4.57121231 Chr04 57121231 QHGHT4.16
QHGHT4.13		 Mocoeur et al. 2015
Nagaraja Reddy et al. 2013		 E-Tian/Ji2731
M35-1/B35		 Height (plant height)
Height (plant height)		 4:53628830-61766744
4:55962847-61572196
QTN4.62261029 Chr04 62261029
QTN4.63570248 Chr04 63570248
QTN4.65266850 Chr04 65266850
QTN4.65863171 Chr04 65863171
QTN5.225941 Chr05 225941
QTN5.17438732 Chr05 17438732 QHGHT5.6 Shiringani et al. 2010 M71/SS79 Height (plant height) 5:11107972-52515528
QTN5.20666756 Chr05 20666756
QTN5.35025393 Chr05 35025393
QTN5.61015103 Chr05 61015103 QINTN5.1 Zhao et al. 2016 Sorghum Association Panel (SAP) Internode number 5:60730347-61689875
QTN5.65444056 Chr05 65444056
QTN5.70860912 Chr05 70860912
QTN6.6070840 Chr06 6070840 QHGHT6.7 Wang et al. 2012 mini-core set Height (plant height) 6:4424055-7760215
QTN6.6720303 Chr06 6720303
QTN6.11512672 Chr06 11512672 QHGHT6.5
QHGHT6.6		 Brown et al. 2006
Feltus et al. 2006		 BTx623/IS3620C Height (plant height) 6:3153035-14654536
6:3472068-20655330
QTN6.14112048 Chr06 14112048 QHGHT6.5 Brown et al. 2006 BTx623/IS3620C Height (plant height) 6:3153035-14654536
QTN6.17354113 Chr06 17354113 QHGHT6.6
 Feltus et al. 2006
 BTx623/IS3620C
 Height (plant height)
 6:3472068-20655330
QTN6.19368812 Chr06 19368812
QTN6.20384517 Chr06 20384517
QTN6.21804125 Chr06 21804125 QSILN6.1 Hilley et al. 2016 Hegari/80M Stem internode length 6:21205500-44995144
QTN6.30195457 Chr06 30195457 QHGHT6.83
QHGHT6.89		 Zhao et al. 2016
Yamaguchi et al. 2016		 Sorghum Association Panel (SAP)
bmr-6/SIL-05		 Height (plant height) 6:27834658-38482472
6:22445901-43378078
QTN6.39969911 Chr06 39969911 QHGHT6.89 Yamaguchi et al. 2016 bmr-6/SIL-05 Height (plant height)
6:22445901-43378078
QTN6.47858747 Chr06 47858747 QHGHT6.58 Srinivas et al. 2009 296B/IS18551 Height (plant height) 6:47229819-48711265
QTN6.51781734 Chr06 51781734 QHGHT6.63 Kebede et al. 2001 SC56/Tx7000 Height (plant height) 6:51611228-52465988
QTN6.58083889 Chr06 58083889 QPLEN6.19 Parh 2005 IS8525/R931945-2-2 Panicle length 6:56618606-61260478
QTN7.1772505 Chr07 1772505
QTN7.2186032 Chr07 2186032
QTN7.26630649 Chr07 26630649 QHGHT7.8 Rami et al. 1998 IS2807/379 Height (plant height) 7:10020434-53294723
QTN7.42714173 Chr07 42714173 QHGHT7.8
QHGHT7.11		 Rami et al. 1998
Madhusudhana and Patil 2013		 IS2807/379
296B/IS18551		 Height (plant height) 7:10020434-53294723
7:42199948-57729128
QTN7.49687684 Chr07 49687684
QTN7.55183398 Chr07 55183398 QHGHT7.11 Madhusudhana and Patil 2013 296B/IS18551 Height (plant height) 7:42199948-57729128
QHGHT7.14 Madhusudhana and Patil 2013 296B/IS18551 Height (plant height) 7:52284804-57820875
QSILN7.1 Hilley et al. 2016 Hegari/80M Stem internode length 7:53924374-57857968
QTN7.56139617 Chr07 56139617 QHGHT7.14
QHGHT7.15		 Madhusudhana and Patil 2013
Srinivas et al. 2009		 296B/IS18551
 Height (plant height) 7:52284804-57820875
7:55190663-57760757
QTN7.58438538 Chr07 58438538 QHGHT7.66
QHGHT7.67		 Wang et al. 2016 Shihong137/L-Tian Height (plant height) 7:57683232-58901776
7:57716834-58775268
QTN7.59393707 Chr07 59393707 QHGHT7.91
QHGHT7.45
QHGHT7.76
QHGHT7.46
QHGHT7.83		 Liu et al. 2019
Pereira and Lee 1995
Yamaguchi et al. 2016
Madhusudhana and Patil 2013
Girma et al. 2019		 Tx623 x S. virgatum
CK60/PI229828
bmr-6/SIL-05
296B/IS18551
Ethiopian landraces		 Height (plant height) 7:59257250-61520522
7:59531861-61538775
7:59541977-61443045
7:59551731-61527847
7:59554149-61141251
QTN7.59653890 Chr07 59653890
QTN7.59721216 Chr07 59721216
QTN7.60501279 Chr07 60501279
QTN7.60940816 Chr07 60940816
QTN7.62144455 Chr07 62144455 QHGHT7.57 Parh 2005 IS8525/R931945-2-2 Height (plant height) 7:61806978-65460255
QHGHT7.55 Madhusudhana and Patil 2013 296B/IS18551 Height (plant height) 7:61910344-63327593
QHGHT7.56 Feltus et al. 2006 BTx623/S. propinquum Height (plant height) 7:61971712-64586189
QTN8.2105446 Chr08 2105446 QSLEN8.1 Wang et al. 2014b Shihong137/L-Tian Shoot length (seedling stage) 8:1896920-3249436
QTN8.4977795 Chr08 4977795
QTN8.8249188 Chr08 8249188
QHGHT8.2
 Shiringani et al. 2010 M71/SS79 Height (plant height) 8:8198323-56470074
QTN8.8955240 Chr08 8955240
QTN8.13232192 Chr08 13232192
QTN8.13747177 Chr08 13747177
QTN8.18073491 Chr08 18073491
QTN8.46279959 Chr08 46279959
QTN8.50392737 Chr08 50392737
QTN8.57976551 Chr08 57976551 QHGHT8.4 Shehzad and Okuno 2015 Red Kafir/Takakibi (F2) Height (plant height) 8:56697504-59292212
QTN8.59708198 Chr08 59708198 qCNN8.1 xu et al. 2023 BTx623/HYZ Internode number 8:58253026—60762263
QTN8.60514221 Chr08 60514221
QTN8.61141049 Chr08 61141049
QTN9.9011331 Chr09 9011331
QHGHT9.5
Nagaraja Reddy et al. 2013
M35-1/B35
Height (plant height)
9:8157572-47755439
QTN9.9723995 Chr09 9723995
QTN9.13457659 Chr09 13457659
QTN9.14023575 Chr09 14023575
QTN9.16091197 Chr09 16091197
QTN9.21770577 Chr09 21770577
QTN9.24272625 Chr09 21554218
QTN9.26282863 Chr09 26282863
QTN9.40913786 Chr09 40913786
QTN9.45916233 Chr09 45916233
QTN9.51292519 Chr09 51292519 QHGHT9.7
QHGHT9.80		 Shiringani et al. 2010
Gelli et al. 2016		 M71/SS79
CK60/China17		 Height (plant height) 9:50633456-52598530
9:50718886-51490320
QTN9.53210328 Chr09 53210328 QHGHT9.8
QHGHT9.10
QHGHT9.75		 Feltus et al. 2006
Lin et al. 1995
Bai et al. 2017		 BTx623/S.propinquum
BTx623/S. propinquum
BTx623/Rio		 Height (plant height)
 9:51845427-56983864
9:52500363-57941639
9:52719464-55273795
QTN9.59349793 Chr09 59349793 QHGHT9.79 Yamaguchi et al. 2016 bmr-6/SIL-05 Height (plant height) 9:59192467-59398238
QTN10.1694341 Chr10 1694341 QHGHT10.13 Mocoeur et al. 2015 E-Tian/Ji2731 Height (plant height) 10:1518275-8359099
QTN10.3945045 Chr10 3945045
QTN10.12448273 Chr10 12448273 QHGHT10.16 Kong et al. 2018 BTx623/IS3620C Height (plant height) 10:10627652-13583029
QTN10.12598609 Chr10 12598609
QTN10.13745644 Chr10 13745644 QHGHT10.17
QHGHT10.5
QHGHT10.18		 Liu et al. 2019
Shiringani et al. 2010
Liu et al. 2019		 Tx623 x S. virgatum
M71/SS79
Tx623 x S. virgatum		 Height (plant height)
Height (plant height)
Height (plant height)		 10:8044545-51747348
10:8640125-45554247
10:9185221-52571741
QTN10.19774145 Chr10 19774145
QTN10.34601077 Chr10 34601077
QTN10.26748555 Chr10 26748555
QTN10.55997217 Chr10 55997217 QHGHT10.14 Mocoeur et al. 2015 E-Tian/Ji2731 Height (plant height) 10:52112522-56441485
QHGHT10.8 Madhusudhana and Patil 2013 296B/IS18551 Height (plant height) 10:52619425-56427175
QTN10.57784636 Chr10 57784636 QHGHT10.11 Rajkumar et al. 2013 E36-1/SPV570 Height (plant height) 10:56548575-60429301
QTN10.60576093 Chr10 60576093
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