Identification of Rice Plant Height-associated QTL Using BSA-seq and RNA-seq

doi:10.13560/j.cnki.biotech.bull.1985.2023-0386

Abstract

Abstract:

The stability of rice yield is significantly influenced by plant height, making it as a crucial factor. The identification of plant height-associated QTLs and mining of candidate genes are conducive to comprehending the molecular regulatory mechanisms that determines plant height, which may lay a foundation for breeding ideal rice varieties. This study employed 285 CSSL populations derived from the parental strains of Oryza sativa var. Youzhan 8 and wild rice from Guangxi as the experimental cohort. The study utilized SNP and InDel molecular markers, in conjunction with NGS and BSA-seq techniques, to conduct an association analysis aimed at identifying genomic regions that are potentially associated with plant height. As results, the molecular markers Δ（SNP-index）were discovered to have an association with candidate genomic regions of 3.205 and 1.311 Mb in Chr.7 and Chr.10, respectively. The genomic regions linked with Δ（InDel-index）markers were of sizes 2.848 and 1.292 Mb, and were entirely encompassed within the intervals associated with Δ（SNP-index）. Through the integration of functional annotation in GO, KEGG, Uniprot, and eggNOG databases, as well as high-quality polymorphic site screening and existing transcriptome data pertaining to plant height, five candidate genes located in Chr.7 were ultimately linked to this trait, including the previously characterized OsTCP21 function and mechanism. The qRT-PCR findings were consistent with prior research, revealing differential expression of OsTCP21 in tall and dwarf plants. Specifically, LOC_Os07g05050 and LOC_Os07g02850 demonstrated elevated expressions in tall plants, whereas LOC_Os07g04220 and LOC_Os07g02770 had higher expressions in dwarf plants. The regulation of rice plant height is significantly influenced by five candidate genes, with OsTCP21 being identified as a pivotal regulatory gene.

Key words: rice, plant height, mapping, BSA-seq, RNA-seq

WU Yuan-ming, LIN Jia-yi, LIU Yu-xi, LI Dan-ting, ZHANG Zong-qiong, ZHENG Xiao-ming, PANG Hong-bo. Identification of Rice Plant Height-associated QTL Using BSA-seq and RNA-seq[J]. Biotechnology Bulletin, 2023, 39(8): 173-184.

Figures/Tables 11

References 52

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样品Sample	原始数据 Raw base/bp	过滤后的有效数据 Clean base/bp	比对率Mapping rate/%	平均测序深度Average depth（×）	至少覆盖1个碱基的位点的比例Coverage at least 1×/%	至少覆盖4个碱基的位点的比例Coverage at least 4×/%	Phred 数值大于20的碱基比例Q20/%	Phred 数值大于30的碱基比例Q30/%	碱基G和C的含量GC/%
YZ8	11 134 196 100	11 134 054 800	99.00	23.81	82.46	79.06	97.57	93.31	44.60
GCWR	14 338 273 200	14 338 088 700	98.65	28.82	85.26	82.67	97.78	93.79	44.23
H-pool	5 067 688 200	5 067 637 200	99.04	11.36	82.27	74.08	97.11	92.15	43.59
L-pool	4 969 848 300	4 969 806 000	99.02	11.43	81.81	74.14	97.14	92.13	43.61

样品Sample	原始数据 Raw base/bp	过滤后的有效数据 Clean base/bp	比对率Mapping rate/%	平均测序深度Average depth（×）	至少覆盖1个碱基的位点的比例Coverage at least 1×/%	至少覆盖4个碱基的位点的比例Coverage at least 4×/%	Phred 数值大于20的碱基比例Q20/%	Phred 数值大于30的碱基比例Q30/%	碱基G和C的含量GC/%
YZ8	11 134 196 100	11 134 054 800	99.00	23.81	82.46	79.06	97.57	93.31	44.60
GCWR	14 338 273 200	14 338 088 700	98.65	28.82	85.26	82.67	97.78	93.79	44.23
H-pool	5 067 688 200	5 067 637 200	99.04	11.36	82.27	74.08	97.11	92.15	43.59
L-pool	4 969 848 300	4 969 806 000	99.02	11.43	81.81	74.14	97.14	92.13	43.61

染色体 Chromosome	起始位置 Start/bp	终止位置 End/bp	大小 Size/Mb	基因数量 Gene number
7	1	2 848 000	2.848	141
10	3 796 001	5 088 000	1.292	135
总计Total	-	-	4.140	276

染色体 Chromosome	起始位置 Start/bp	终止位置 End/bp	大小 Size/Mb	基因数量 Gene number
7	1	2 848 000	2.848	141
10	3 796 001	5 088 000	1.292	135
总计Total	-	-	4.140	276

基因 Gene ID	基因注释 Gene annotation
LOC_Os07g02770	含F-box和亮氨酸富集重复序列的蛋白 Protein containing F-box and leucine-enriched repeats
LOC_Os07g02850	含DUF538结构域的蛋白 Protein containing DUF538 domain
LOC_Os07g04220	光敏色素信号与损伤相关的受体类激酶 Wound and phytochrome signaling involved receptor like kinase
LOC_Os07g05050	含DEAD-box的ATP依赖的RNA解旋酶 ATP-dependent RNA helicase containing DEAD-box
LOC_Os07g05720	TCP转录因子 TCP family transcription factor