Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Pan, Zhaoyuan; Tan, Bin; Cao, Guiyuan; Zheng, Rongqi; Liu, Meng; Zeng, Ruizhen; Wang, Shaokui; Zhu, Haitao; Ye, Heng; Zhao, Guangmiao; Cao, Wei; Liu, Guifu; Zhang, Guiquan; Zhou, Yuliang

doi:10.1186/s12284-021-00544-2

Rice

Table 3 Function annotation, sequence variation and gene expression of candidate genes in the qLTG3a region

From: Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Gene RAP ID^a	Gene function ^b	Indel number*	SNP number*	Gene expression level in seeds ^c
Os03g0213300	Phosphopantetheine attachment site domain containing protein; Hypothetical conserved gene	1	3	High
Os03g0213400	Similar to RNA helicase			Medium
Os03g0213500	Conserved hypothetical protein			High
Os03g0213600	Conserved hypothetical protein	3	3	Medium
Os03g0213700	DUF647 domain containing protein	1		Medium
Os03g0213800	Mitochondrial substrate carrier family protein	2		Medium
Os03g0213900	Conserved hypothetical protein; ROUGH SHEATH2-interacting KH-domain protein	3	3	Medium
Os03g0214000	Diphosphonucleotide phosphatase 1 precursor; nucleotide pyrophosphatase	1		High
Os03g0214050	Hypothetical protein			no data
Os03g0214100	Replication protein A1		1	Low
Os03g0214200	Mediator of OsbZIP46 deactivation and degradation, Negative regulation of ABA signaling and drought tolerance; Ninja-family protein 1			Medium
Os03g0214400	Digalactosyldiacylglycerol synthase 2	4		High
Os03g0214600	26S proteasome subunit RPN9a; 26S proteasome non-ATPase regulatory subunit 13	2		High
Os03g0214900	Conserved hypothetical protein	4	2	Medium
Os03g0215000	Integral membrane family protein			High
Os03g0215200	Putative transcription factor, Carpel specification, Midrib formation			Low
Os03g0215400	MADS-domain-containing protein, sexual reproduction	1		Medium
Os03g0215600	Zinc finger, CCHC retroviral-type domain containing protein			Very low
Os03g0215700	Myosin II heavy chain-like family protein	3	1	Very low
Os03g0215800	Pyridoxal phosphate-dependent enzyme	1		Low
Os03g0215900	67kD chloroplastic RNA-binding protein, P67			Low
Os03g0216000	Zinc-finger protein KNUCKLES			Very low
Os03g0216300	Pentatricopeptide repeat domain containing protein; Hypothetical conserved gene	1		Low
Os03g0216400	Pentatricopeptide repeat domain containing protein			Low
Os03g0216500	Conserved hypothetical protein		1	Low
Os03g0216600	Alpha-glucosidase (EC 3.2.1.20)			High
Os03g0216700	Citrate transporter, Efficient translocation of Fe	1		Medium
Os03g0216733	Hypothetical protein			no data
Os03g0216766	Hypothetical gene			no data
Os03g0216800	Polygalacturonase B (Fragment)	1	1	Very low
Os03g0216900	Prefoldin domain containing protein			Low
Os03g0217000	Inhibin beta B chain precursor		1	Low
Os03g0217200	Cyclin-like F-box domain containing protein			Medium
Os03g0217400	Conserved hypothetical protein			Low
Os03g0217801	Hypothetical gene			no data
Os03g0217900	Hypothetical protein			Medium
Os03g0218100	Sec63 domain containing protein			no data
Os03g0218200	F-box domain containing protein	1		Low
Os03g0218300	Conserved hypothetical protein		3	Medium
Os03g0218400	Similar to Hexose transporter			Low

*Sequence variation analysis of candidate genes was derived from BSA sequencing data. The number of InDels was derived from the upstream and exonic regions of the candidate genes, and the number of SNPs was derived from the nonsynonymous SNPs in the exonic regions. The ΔSNP-index and ΔInDel-index were greater than 0.8
^a^,bRAP ID and gene function are based on the Rice Annotation Project Database (RAP-DB): http://rapdb.dna.affrc.go.jp
^cThe expression level of candidate genes in seeds was analyzed by the public tool RiceXPro (http://ricexpro.dna.affrc.go.jp/) and divided into four levels

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