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Chen H, Zhai L, Chen K, Shen C, Zhu S, Qu P, Tang J, Liu J, He H, Xu J. Genetic background- and environment-independent QTL and candidate gene identification of appearance quality in three MAGIC populations of rice. Front Plant Sci 2022; 13:1074106. [PMID: 36438096 PMCID: PMC9697191 DOI: 10.3389/fpls.2022.1074106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/28/2022] [Indexed: 06/01/2023]
Abstract
Many QTL have been identified for grain appearance quality by linkage analysis (LA) in bi-parental mapping populations and by genome-wide association study (GWAS) in natural populations in rice. However, few of the well characterized genes/QTL have been successfully applied in molecular rice breeding due to genetic background (GB) and environment effects on QTL expression and deficiency of favorable alleles. In this study, GWAS and LA were performed to identify QTL for five grain appearance quality-related traits using three multi-parent advanced generation inter-cross (MAGIC) populations. A total of 22 QTL on chromosomes 1-3, 5-8 were identified by GWAS for five traits in DC1, DC2 and 8way, and four combined populations DC12 (DC1+DC2), DC18 (DC1+8way), DC28 (DC2+8way) and DC128 (DC1+DC2+8way). And a total of 42 QTL were identified on all 12 chromosomes except 10 by LA in the three single populations. Among 20 QTL identified by GWAS in DC1, DC2 and 8way, 10, four and three QTL were commonly detected in DC18, DC28, and DC128, respectively. Similarly, among 42 QTL detected by LA in the three populations, four, one and two QTL were commonly detected in DC18, DC28, and DC128, respectively. There was no QTL mapped together in DC12 by both two mapping methods, indicating that GB could greatly affect the mapping results, and it was easier to map the common QTL among populations with similar GB. The 8way population was more powerful for QTL mapping than the DC1, DC2 and various combined populations. Compared with GWAS, LA can not only identify large-effect QTL, but also identify minor-effect ones. Among 11 QTL simultaneously detected by the two methods in different GBs and environments, eight QTL corresponded to known genes, including AqGL3b and AqGLWR3a for GL and GLWR, AqGW5a, AqGLWR5, AqDEC5 and AqPGWC5 for GW, GLWR, DEC and PGWC, and AqDEC6b and AqPGWC6b for DEC and PGWC, respectively. AqGL7, AqGL3c/AqGLWR3b, AqDEC6a/AqPGWC6a, and AqPGWC7 were newly identified and their candidate genes were analyzed and inferred. It was discussed to further improve grain appearance quality through designed QTL pyramiding strategy based on the stable QTL identified in the MAGIC populations.
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Affiliation(s)
- Huizhen Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Pingxiang Center for Agricultural Sciences and Technology Research, Pingxiang, Jiangxi, China
| | - Laiyuan Zhai
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Congcong Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shuangbing Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Pingping Qu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Tang
- Pingxiang Center for Agricultural Sciences and Technology Research, Pingxiang, Jiangxi, China
| | - Jianping Liu
- Pingxiang Center for Agricultural Sciences and Technology Research, Pingxiang, Jiangxi, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Jianlong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Zafar S, You H, Zhang F, Zhu SB, Chen K, Shen C, Wu H, Zhu F, Zhang C, Xu J. Genetic dissection of grain traits and their corresponding heterosis in an elite hybrid. Front Plant Sci 2022; 13:977349. [PMID: 36275576 PMCID: PMC9581170 DOI: 10.3389/fpls.2022.977349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Rice productivity has considerably improved due to the effective employment of heterosis, but the genetic basis of heterosis for grain shape and weight remains uncertain. For studying the genetic dissection of heterosis for grain shape/weight and their relationship with grain yield in rice, quantitative trait locus (QTL) mapping was performed on 1,061 recombinant inbred lines (RILs), which was developed by crossing xian/indica rice Quan9311B (Q9311B) and Wu-shan-si-miao (WSSM). Whereas, BC1F1 (a backcross F1) was developed by crossing RILs with Quan9311A (Q9311A) combined with phenotyping in Hefei (HF) and Nanning (NN) environments. Overall, 114 (main-effect, mQTL) and 359 (epistatic QTL, eQTL) were identified in all populations (RIL, BC1F1, and mid-parent heterosis, HMPs) for 1000-grain weight (TGW), grain yield per plant (GYP) and grain shape traits including grain length (GL), grain width (GW), and grain length to width ratio (GLWR). Differential QTL detection revealed that all additive loci in RILs population do not show heterotic effects, and few of them affect the performance of BC1F1. However, 25 mQTL not only contributed to BC1F1's performance but also contributed to heterosis. A total of seven QTL regions was identified, which simultaneously affected multiple grain traits (grain yield, weight, shape) in the same environment, including five regions with opposite directions and two regions with same directions of favorable allele effects, indicating that partial genetic overlaps are existed between different grain traits. This study suggested different approaches for obtaining good grain quality with high yield by pyramiding or introgressing favorable alleles (FA) with the same direction of gene effect at the QTL regions affecting grain shape/weight and grain yield distributing on different chromosomes, or introgressing or pyramiding FA in the parents instead of fixing additive effects in hybrid as well as pyramiding the polymorphic overdominant/dominant loci between the parents and eliminating underdominant loci from the parents. These outcomes offer valuable information and strategy to develop hybrid rice with suitable grain type and weight.
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Affiliation(s)
- Sundus Zafar
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui You
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuang Bin Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Congcong Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hezhou Wu
- Hunan Tao-Hua-Yuan Agricultural Technologies Co., LTD., Hunan, China
| | - Fangjin Zhu
- Hunan Tao-Hua-Yuan Agricultural Technologies Co., LTD., Hunan, China
| | | | - Jianlong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Hainan Yazhou Bay Seed Lab/National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Obara M, Fukuta Y, Yanagihara S. Genetic variation and QTLs related to root development in upland New Rice for Africa (NERICA) varieties. Breed Sci 2019; 69:94-103. [PMID: 31086487 PMCID: PMC6507723 DOI: 10.1270/jsbbs.18059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/20/2018] [Indexed: 06/09/2023]
Abstract
To understand variation in the root development traits (total root length (TRL), maximum root length (MRL) and root number) of 18 New Rice for Africa (NERICA) varieties, seedlings were hydroponically grown under deficient and sufficient concentrations of two forms of nitrogen, NH4 + and NO3 -. The donor African rice variety, 'CG14' (Oryza glaberrima Steud.), showed greater TRL and MRL than three background Asian rice varieties (Oryza sativa L.). Wide distribution was observed in all traits of the 18 NERICAs. The 18 NERICAs and parental varieties were classified into three cluster groups by cluster analysis. Cluster Ia included only 'CG14'. Comparative analysis characterized cluster Ib (including 'NERICA7') as an active root elongation group, and cluster II (including 'WAB56-104') as an active primordia development group. QTL analysis of F2 plants developed from a cross between 'WAB56-104' and 'NERICA7' detected two putative quantitative trait loci (QTLs) for root elongation on chromosome 1. Of these, a major QTL, designated as qRL1.4-NERICA7, was an NH4 +-responsive QTL, which was narrowed down to a 0.7-Mbp region through progeny testing using F7 lines. qRL1.4-NERICA7 should help us understand genetic control in NERICAs, and improve root elongation in rice breeding programs.
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Affiliation(s)
- Mitsuhiro Obara
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences,
1-1 Ohwashi, Tsukuba, Ibaraki 305-8686,
Japan
| | - Yoshimichi Fukuta
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences,
1091-1 Kawarabaru, Ishigaki, Okinawa 907-0002,
Japan
| | - Seiji Yanagihara
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences,
1-1 Ohwashi, Tsukuba, Ibaraki 305-8686,
Japan
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Feng B, Chen K, Cui Y, Wu Z, Zheng T, Zhu Y, Ali J, Wang B, Xu J, Zhang W, Li Z. Genetic Dissection and Simultaneous Improvement of Drought and Low Nitrogen Tolerances by Designed QTL Pyramiding in Rice. Front Plant Sci 2018; 9:306. [PMID: 29593764 PMCID: PMC5855007 DOI: 10.3389/fpls.2018.00306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 02/22/2018] [Indexed: 05/13/2023]
Abstract
Drought and low nitrogen are the most common abiotic stresses limiting rice productivity in the rainfed rice areas of Asia and Africa. Development and adoption of green super rice (GSR) varieties with greatly improved drought tolerance (DT) and low nitrogen tolerance (LNT) are the most efficient way to resolve this problem. In this study, using three sets of trait-specific introgression lines (ILs) in a Xian (indica) variety Huanghuazhan (HHZ) background, we identified nine DT-QTL and seven LNT-QTL by a segregation distortion approach and a genome-wide association study, respectively. Based on performances of DT and LNT and genotypes at the detected QTL, two ILs M79 and M387 with DT and LNT were selected for cross-making to validate the identified QTL and to develop DT and LNT rice lines by pyramiding two DT-QTL (qDT3.9 and qDT6.3) and two LNT-QTL (qGY1 and qSF8). Using four pairs of kompetitive allele specific PCR (KASP) SNP markers, we selected 66 F2 individuals with different combinations of the target DT- and LNT-QTL favorable alleles and they showed expected improvement in DT and/or LNT, which were further validated by the significant improvement in DT and/or LNT of their F3 progeny testing. Based on evaluation of pyramiding lines in F3 lines under drought, low nitrogen (LN) and normal conditions, four promising pyramiding lines having different QTL favorable alleles were selected, which showed significantly improved tolerances to drought and/or LN than HHZ and their IL parents. Our results demonstrated that trait-specific ILs could effectively connect QTL mapping and QTL pyramiding breeding, and designed QTL pyramiding (DQP) using ILs could be more effective in molecular rice breeding for complex quantitative traits.
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Affiliation(s)
- Bo Feng
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education, Shenyang, China
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kai Chen
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yanru Cui
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhichao Wu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianqing Zheng
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yajun Zhu
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jauhar Ali
- International Rice Research Institute, Los Baños, Philippines
| | | | - Jianlong Xu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wenzhong Zhang
- Rice Research Institute, Shenyang Agricultural University, Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education, Shenyang, China
| | - Zhikang Li
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen, China
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