QTL Mapping and Candidate Gene Analysis on Rice Leaf Water Potential

doi:10.11983/CBB21039

Abstract

Abstract: To reveal the role and genetic mechanism of genes related to leaf water potential (LWP) in rice drought resistance, the 120 recombinant inbred lines (RILs) populations derived from the cross of Nekken2 and HZ as well as the two parents were chosen as the experiment materials in this study. After testing and analyzing the leaf water potential at tillering stage, quantitative trait loci (QTL) were detected based on the molecular linkage map of these populations constructed by using high-throughput sequencing in the early stage. The experimental results showed that 5 QTLs related to leaf water potential at tillering stage were located on chromosome 2, 3, 4, 11 and 12, respectively, with LOD (likelihood of odd) value all above 2.5, one of which located on chromosome 4 with physical distance between 24 066 261 and 30 847 136 bp showed the highest LOD value of 5.15. Through quantitative analysis of these candidate genes relevant to leaf water potential within the QTL regions, 7 genes, LOC_Os02g56630, LOC_Os02g57720, LOC_Os02g57580, LOC_ Os04g43730, LOC_Os04g46490, LOC_Os04g44570, LOC_Os04g44060, were identified to have different expression levels between the two parents. LOC_Os04g46490, which located within the QTL region on chromosome 4, showed significant difference in gene expression and 6 differences at DNA sequences and changes at amino acids between two parents. By QTL mining and quantitative analysis of related genes, we discovered that these genes were associated with the regulation of leaf water potential, which may indirectly affect the drought resistance of rice. The detected QTL loci have important reference value for QTL fine mapping and genes cloning associated with drought tolerance, thus facilitating our understanding of the genetic basis of rice leaf water potential, and providing genetic resources for developing new drought-tolerant rice cultivars.

Key words: rice, leaf water potential, drought resistance, genetic map, QTL mapping

Chenyang Pan, Yue Zhang, Han Lin, Qianyu Chen, Kairu Yang, Jiaji Jiang, Mengjia Li, Tao Lu, Kexin Wang, Mei Lu, Sheng Wang, Hanfei Ye, Yuchun Rao, Haitao Hu. QTL Mapping and Candidate Gene Analysis on Rice Leaf Water Potential[J]. Chinese Bulletin of Botany, 2021, 56(3): 275-283.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB21039

https://www.chinbullbotany.com/EN/Y2021/V56/I3/275

Figures/Tables 8

References 28

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Primer name	Sequence (5′-3′)	Tm (°C)	Length (bp)
LOC_Os02g56630-F-qrt	GATGCTACGGAGACTGCACA	60.02	182
LOC_Os02g56630-R-qrt	GAGCCAGAAGCACATGAACA	59.99	182
LOC_Os02g57720-F-qrt	CTGACGTCGTGGTCGTTCTA	59.90	101
LOC_Os02g57720-R-qrt	GACTTGTTCACCCCCATCAC	60.22	101
LOC_Os04g43730-F-qrt	ACCAAAGTGGGTGTTTCTCG	60.01	153
LOC_Os04g43730-R-qrt	TCGAGATCTGGCTTGTGTTG	59.98	153
LOC_Os04g44060-F-qrt	CGGTGTTCATGGTTCACTTG	60.00	182
LOC_Os04g44060-R-qrt	CCTCAGGACGTACTGGTGGT	60.03	182
LOC_Os04g46490-F-qrt	GCCTCGTCCTCCACTACATC	59.69	123
LOC_Os04g46490-R-qrt	CCGTGTACACCACCATGAAC	59.73	123
LOC_Os02g57580-F-qrt	ACCTCTTCAGATGGGGTGTG	59.96	101
LOC_Os02g57580-R-qrt	CCAGTCAGTTTTGCAGACCA	59.87	101
LOC_Os04g48230-F-qrt	GGGCACTACAAGTCCGTGAT	60.00	199
LOC_Os04g48230-R-qrt	CTTGGTAGCTTCCGATGAGC	59.98	199
LOC_Os04g44570-F-qrt	CGCCACCACTGGGTTTACT	60.96	123
LOC_Os04g44570-R-qrt	CACGGGAAGCCGAGTATCT	60.23	123

Primer name	Sequence (5′-3′)	Tm (°C)	Length (bp)
LOC_Os02g56630-F-qrt	GATGCTACGGAGACTGCACA	60.02	182
LOC_Os02g56630-R-qrt	GAGCCAGAAGCACATGAACA	59.99	182
LOC_Os02g57720-F-qrt	CTGACGTCGTGGTCGTTCTA	59.90	101
LOC_Os02g57720-R-qrt	GACTTGTTCACCCCCATCAC	60.22	101
LOC_Os04g43730-F-qrt	ACCAAAGTGGGTGTTTCTCG	60.01	153
LOC_Os04g43730-R-qrt	TCGAGATCTGGCTTGTGTTG	59.98	153
LOC_Os04g44060-F-qrt	CGGTGTTCATGGTTCACTTG	60.00	182
LOC_Os04g44060-R-qrt	CCTCAGGACGTACTGGTGGT	60.03	182
LOC_Os04g46490-F-qrt	GCCTCGTCCTCCACTACATC	59.69	123
LOC_Os04g46490-R-qrt	CCGTGTACACCACCATGAAC	59.73	123
LOC_Os02g57580-F-qrt	ACCTCTTCAGATGGGGTGTG	59.96	101
LOC_Os02g57580-R-qrt	CCAGTCAGTTTTGCAGACCA	59.87	101
LOC_Os04g48230-F-qrt	GGGCACTACAAGTCCGTGAT	60.00	199
LOC_Os04g48230-R-qrt	CTTGGTAGCTTCCGATGAGC	59.98	199
LOC_Os04g44570-F-qrt	CGCCACCACTGGGTTTACT	60.96	123
LOC_Os04g44570-R-qrt	CACGGGAAGCCGAGTATCT	60.23	123

QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
qLpw2-8	2	34636269-35675126	148.48-152.93	3.27
qLpw3-8	3	30389734-30481217	130.27-130.66	2.93
qLpw4-8	4	24066261-30847136	103.17-132.23	5.15
qLpw11-8	11	2051418-2119803	8.79-9.09	3.06
qLpw12-8	12	25396321-25626163	108.87-109.85	3.34

QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
qLpw2-8	2	34636269-35675126	148.48-152.93	3.27
qLpw3-8	3	30389734-30481217	130.27-130.66	2.93
qLpw4-8	4	24066261-30847136	103.17-132.23	5.15
qLpw11-8	11	2051418-2119803	8.79-9.09	3.06
qLpw12-8	12	25396321-25626163	108.87-109.85	3.34

Chromosome	Gene	Function	Regulation object	Reference
2	LOC_Os02g56630	Play an important regulatory role in the response of plants to abiotic stress	OsWAK24-OsWAK receptor-like protein kinase
4	LOC_Os04g43730	Play an important regulatory role in the response of plants to abiotic stress	OsWAK51-OsWAK receptor-like protein kinase
2	LOC_Os02g57580	Maybe involved in anthocyanin vacuole storage, participate in osmotic adjustment	Anthocyanin permease	Aza-González et al., 2013
2	LOC_Os02g57720	Mediate the transport of water across the membrane, regulate water	Aquaporin
4	LOC_Os04g46490	Mediate the transport of water across the membrane, regulate water	Aquaporin
4	LOC_Os04g44570	Mediate the transport of water across the membrane, regulate water	Aquaporin
4	LOC_Os04g44060	Mediate the transport of water across the membrane, regulate water	Aquaporin
4	LOC_Os04g48230	Maybe involved in the perception, conduc- tion of plant dehydration and regulation of antidehydration substance synthesis	Dehydration response related protein	Shinozaki and Yamaguchi-Shinozaki, 1997