Scientia Agricultura Sinica ›› 2024, Vol. 57 ›› Issue (21): 4192-4204.doi: 10.3864/j.issn.0578-1752.2024.21.003

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Comparison of the Genome Sequence Polymorphisms Between the Main Naked Barley Varieties Kunlun 14 and Kunlun 15 in Qinghai Province

XU JinQing1(), BIAN HaiYan1,2, CHEN TongRui1,2, WANG Lei1, WANG HanDong1, YOU En1,2, DENG Chao1,2, TANG YouLin1, SHEN YuHu1,3()   

  1. 1 Northwest Institute of Plateau Biology, Chinese Academy of Sciences/Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB)/Qinghai Provincial Key Laboratory of Crop Molecular Breeding/Laboratory for Research and Utilization of Qinghai-Tibetan Plateau Germplasm Resources, Xining 810008
    2 College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049
    3 Innovation Academy for Seed Design (INASEED), Chinese Academy of Sciences, Xining 810008
  • Received:2024-05-02 Accepted:2024-07-12 Online:2024-11-01 Published:2024-11-10

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Abstract:

【Objective】At present, Kunlun 14 and Kunlun 15 are the main varieties of the naked barley in Qinghai Province, and also the important backbone parents in the breeding of the naked barley. The genomic sequences of Kunlun 14 and Kunlun 15 were compared to provide references for the trace of important character regions/loci, pedigree analysis and their utilization in molecular design breeding of the naked barley. 【Method】In this study, the agronomic and grain traits of Kunlun 14 and Kunlun 15 were investigated in the field, and the whole genome resequencing were performed (sequencing depth ≥15×). The sequence differences of copy number variation (CNV), single nucleotide polymorphism (SNP) and insertion/deletion (InDel) were compared between the two varieties. According to the SNP distribution patterns, the polymorphism hotspot and genetic similar regions between them were identified. The mutation types of polymorphism hotspot and genetic similar regions were compared and analyzed. The gene enrichment analysis was carried out in the specific CNV regions and the polymorphism hotspots regions of the two varieties. 【Result】In addition to the plant height and peduncle internode length, Kunlun 14 and Kunlun 15 had high similarity in important agronomic and grain traits. Compared with the barley reference genome of Morex, the two varieties had a common CNV variation interval of 83 Mb, and the length of cultivar-specific CNV variation interval in Kunlun 14 and Kunlun 15 was 37 Mb and 38 Mb, respectively. There were 564 genes in the CNV region specific to Kunlun 14, which were significantly enriched in 15 GO terms, while 519 genes were in the CNV region specific to Kunlun 15 and were significantly enriched in 7 GO terms. Based on the SNP distribution patterns, 1 706 Mb polymorphism hotspots and 2 411 Mb sequence similarity intervals of Kunlun 14 and Kunlun 15 were identified at the whole genome level, and the polymorphism hotspots were mainly distributed on 3H, 6H and 7H. The polymorphism hotspots regions contained 16 768 genes, whose functions were mainly related to plant growth and development. There was no significant difference between polymorphism hotspot regions and genetic similar regions in SNP variation type, InDel length distribution and the proportion of mutations affecting coding function. The SNPs and InDel mutations in polymorphism hotspot and genetic similar regions were mainly missense mutations and followed by synonymy mutations. 【Conclusion】The field phenotypes of Kunlun 14 and Kunlun 15 were similar. At the whole genome level, a total of 75 Mb CNV variation regions between them and the polymorphism hotspot regions were mainly distributed at 3H, 6H and 7H.

Key words: naked barley (Hordeum vulgare var. coeleste L.), Kunlun 14, Kunlun 15, re-sequencing, polymorphism

Fig. 1

Morphological comparison between Kunlun 14 and Kunlun 15 A: Comparison of plant architecture between Kunlun 14 and Kunlun 15; B: Comparison of panicle between Kunlun 14 and Kunlun 15; C: Comparison of kernel between Kunlun 14 and Kunlun 15"

Table 1

Comparison of agronomic traits between Kunlun 14 and Kunlun 15"

表型
Phenotype		 昆仑14
Kunlun 14		 昆仑15
Kunlun 15		 差异显著性
Statistical significance of the difference
均值±标准差
Mean±SE		 变异系数
CV (%)		 均值±标准差
Mean±SE		 变异系数
CV (%)		 P
株高Plant height (cm) 59.91±6.03 10.07 49.48±5.15 10.41 1.51×10-6
穗长Spike length (cm) 8.64±1.14 13.17 8.11±0.76 9.34 0.09
小穗数Spikelet number per spike 23.00±2.00 12.20 23.00±2.00 7.92 0.03
穗粒数Grain number per spike 56.00±7.00 12.47 62.00±8.00 12.24 0.04
穗下节长Peduncle length (cm) 22.16±4.31 19.44 14.11±3.09 21.93 8.89×10-8
千粒重Thousand seed weight (g) 48.71±1.78 3.65 43.20±3.41 7.88 0.068
粒长Grain length (mm) 7.66±0.32 4.14 7.62±0.40 5.27 0.916
粒宽Grain width (mm) 3.69±0.16 4.46 3.57±0.15 4.07 0.389

Table 2

Summary of SNPs and InDels in Kunlun 14 and Kunlun 15"

染色体
Chromosome		 SNP个数No. of SNPs InDel个数No. of InDels
昆仑14 Kunlun 14 昆仑15 Kunlun 15 昆仑14 Kunlun 14 昆仑15 Kunlun 15
1H 2572435 2493453 194793 189090
2H 2213470 2794295 178506 228558
3H 4418644 4449240 315331 325344
4H 3633885 3738124 255476 275711
5H 4332116 4490697 303485 319914
6H 3431778 3850008 244196 277789
7H 5004643 4797651 354226 349414
总计Total 25606971 26613468 1846013 1965820

Table 3

Summary for the CNV regions identified in Kunlun 14 and Kunlun 15"

染色体
Chromosome		 昆仑14的特有CNV变异区间
Specific CNV regions in Kunlun 14		 昆仑15的特有CNV变异区间
Specific CNV regions in Kunlun 15		 两品种的共有CNV变异区间
Common CNV regions in the two cultivars
长度
Length (Mb)		 占比
<BOLD>P</BOLD>ercentage (%)		 长度
Length (Mb)		 占比
<BOLD>P</BOLD>ercentage (%)		 长度
Length (Mb)		 占比
<BOLD>P</BOLD>ercentage (%)
1H 3 0.58 2 0.39 13 2.51
2H 5 0.75 8 1.20 16 2.40
3H 5 0.80 7 1.13 4 0.64
4H 2 0.33 2 0.33 6 0.98
5H 9 1.53 2 0.34 11 1.87
6H 2 0.36 11 1.96 11 1.96
7H 11 1.74 6 0.95 22 3.48
全基因组Whole genome 37 0.88 38 0.90 83 1.98

Fig. 2

GO enrichment analysis of the genes in Kunlun 14 (A) and Kunlun 15 (B) specified CNV regions"

Fig. 3

SNP distribution in the whole genome of Kunlun 14 and Kunlun 15"

Fig. 4

GO enrichment analysis of the genes in the SNP hotpot regions between Kunlun 14 and Kunlun 15"

Fig. 5

Mutation types of SNPs (A) and length distributions of InDels (B) in the polymorphism hotpot regions and genetic similar regions between Kunlun 14 and Kunlun 15"

Table 4

Statistics of the effects on protein coding functions between Kunlun 14 and Kunlun 15"

变异所在区间
Region of
variations		 错义突变
Missense mutation		 同义突变
Synonymous mutation		 提前终止突变
Stop-gained mutation		 终止子丢失突变
Stop-lost mutation		 移码突变
Frame-shift mutation
数量
Count		 占比<BOLD>P</BOLD>ercentage (%) 数量
Count		 占比<BOLD>P</BOLD>ercentage (%) 数量
Count		 占比<BOLD>P</BOLD>ercentage (%) 数量
Count		 占比<BOLD>P</BOLD>ercentage (%) 数量
Count		 占比<BOLD>P</BOLD>ercentage (%)
多态性热点区间
Differential genetic region		 69558 49.83 63210 45.28 1083 0.78 204 0.15 5535 3.97
相似区间
Similar genetic region		 37557 49.61 34190 45.16 734 0.97 161 0.21 3067 4.05
全部 Total 107115 49.75 97400 45.24 1817 0.84 365 0.17 8602 4.00

Table 5

Lists of candidate genes for phenotypic difference between Kunlun 14 and Kunlun 15"

基因
Gene		 基因编号
Gene ID		 位置
Position		 区间
Region		 基因功能注释
Function annotation
HvAP2 HORVU.MOREX.r3.2HG0204770 2H:635314602:635318153 多态性热点区间
Polymorphic hotpot regions		 APETALA2蛋白
APETALA2 protein
HvBRI HORVU.MOREX.r3.3HG0285210 3H:464679001:464682900 多态性热点区间
Polymorphic hotpot regions		 油菜素内酯不敏感蛋白
Brassinosteroid-insensitive protein
Hox12 HORVU.MOREX.r3.4HG0399240 4H:547157498:547158977 序列相似区间
Genetic similar regions		 亮氨酸同源拉链蛋白
Homeobox-leucine zipper protein 12
HORVU.MOREX.r3.2HG0131280 2H:138929371:138930682 序列相似区间
Genetic similar regions		 同源结构域亮氨酸拉链蛋白
Homeodomain leucine zipper protein
GA20ox HORVU.MOREX.r3.3HG0307130 3H:563923790:563926675 多态性热点区间
Polymorphic hotpot regions		 赤霉素20氧化酶
Gibberellin 20 oxidase
HORVU.MOREX.r3.1HG0065220 1H:427826953:427829989 序列相似区间
Genetic similar regions		 赤霉素20氧化酶
Gibberellin 20 oxidase
HORVU.MOREX.r3.5HG0536610 5H:583942988:583944186 序列相似区间
Genetic similar regions		 赤霉素20氧化酶
Gibberellin 20 oxidase

Fig. 6

Annotation of SNPs (A) and InDels (B) in the candidate genes"

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