1
|
Zhang Y, Chen J, Gao Z, Wang H, Liang D, Guo Q, Zhang X, Fan X, Wu Y, Liu Q. Identification of heterosis and combining ability in the hybrids of male sterile and restorer sorghum [Sorghum bicolor (L.) Moench] lines. PLoS One 2024; 19:e0296416. [PMID: 38166022 PMCID: PMC10760902 DOI: 10.1371/journal.pone.0296416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/12/2023] [Indexed: 01/04/2024] Open
Abstract
In sorghum [Sorghum bicolor (L.) Moench], combining ability and heterosis analysis are commonly used to evaluate superior parental lines and to screen for strongly heterotic hybrids, which helps in sorghum variety selection and breeding. In this context, combining ability and heterosis analysis were assessed using 14 restorer lines and seven cytoplasmic male sterile (CMS) lines in 2019 and 2020. The analysis of variance of all cross combinations had highly significant differences for all characters studied, which indicated a wide variation across the parents, lines, testers, and crosses. Combining ability analysis showed that the general combining ability (GCA) and specific combining ability (SCA) of the different parents were differed significantly among different traits. Most combinations with high SCA also showed high GCA in their parent lines. The heritability in the narrow sense of grain weight per panicle and grain yield was relatively low, indicating that the ability of these traits to be directly inherited by offspring was weak, that they were greatly affected by the environment. The better-parent heterosis for plant height, grain weight per panicle, panicle length, and 1000-grain weight was consistent with the order of mid-parent heterosis from strong to weak. The GCA effects of two lines 10480A, 3765A and three testers 0-30R, R111, and JY15R were significant for the majority of the agronomic traits including grain yield and might be used for improving the yield of grains in sorghum as parents of excellent specific combining ability. Seven strongly heterotic F1 hybrids were screened; of these, hybrids 3765A × R111, 1102A × L2R, and 3765A × JY15R showed significant increases in seed iristectorigenin A content and will feature into the creation of new sorghum varieties rich in iristectorigenin A.
Collapse
Affiliation(s)
- Yizhong Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, People’s Republic of China
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci, Shanxi, People’s Republic of China
- National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation), State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, People’s Republic of China
| | - Jing Chen
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, People’s Republic of China
| | - Zhenfeng Gao
- College of Food Science and Engineering, Shanxi Agricultural University, Taiyuan, Shanxi, People’s Republic of China
| | - Huiyan Wang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci, Shanxi, People’s Republic of China
- National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation), State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, People’s Republic of China
| | - Du Liang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci, Shanxi, People’s Republic of China
- National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation), State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, People’s Republic of China
| | - Qi Guo
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci, Shanxi, People’s Republic of China
- National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation), State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, People’s Republic of China
| | - Xiaojuan Zhang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci, Shanxi, People’s Republic of China
- National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation), State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, People’s Republic of China
| | - Xinqi Fan
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci, Shanxi, People’s Republic of China
- National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation), State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, People’s Republic of China
| | - Yuxiang Wu
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, People’s Republic of China
| | - Qingshan Liu
- National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation), State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, People’s Republic of China
| |
Collapse
|
2
|
Wang S, Wu H, Lu Z, Liu W, Wang X, Fang Z, He X. Combining Ability Analysis of Yield-Related Traits of Two Elite Rice Restorer Lines in Chinese Hybrid Rice. Int J Mol Sci 2023; 24:12395. [PMID: 37569770 PMCID: PMC10418745 DOI: 10.3390/ijms241512395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Hybrid rice breeding is an important strategy for enhancing grain yield. Breeding high-performance parental lines and identifying combining abilities is a top priority for hybrid breeding. Yuenongsimiao (YNSM) and its derivative variety Yuehesimiao (YHSM) are elite restorer lines with a high ability of fertility restoration, from which 67 derived hybrid combinations have been authorized to different degrees in more than 110 instances in China. In this study, we found that YNSM and YHSM contained three candidate restorer-of-fertility (Rf) genes, Rf3, Rf4, and Rf5/Rf1a, that might confer their restoration ability. Subsequently, we investigated heterosis and combining ability of YNSM and YHSM using 50 F1 hybrids from a 5 × 10 incomplete diallelic mating design. Our results indicated that hybrid combinations exhibited significant genetic differences, and the additive effects of the parental genes played a preponderant role in the inheritance of observed traits. The metrics of plant height (PH), 1000-grain weight (TGW), panicle length (PL), and the number of spikelets per panicle (NSP) were mainly affected by genetic inheritance with higher heritability. Notably, the general combining ability (GCA) of YHSM exhibited the largest positive effect on the number of grains per panicle (NGP), NSP, PL, and TGW. Thus, YHSM had the largest GCA effect on yield per plant (YPP). In addition, the GCA of YNSM exhibited a positive impact on YPP, mainly due to the critical contribution of seed setting percentage (SSP). Moreover, YNSM and YHSM exhibited negative GCA effects on PH, implying that YNSM and YHSM could effectively enhance plant lodging resistance by reducing the plant height of the derived hybrids. Remarkably, among the hybrids, Yuanxiang A/YNSM (YXA/YNSM), Shen 08S/Yuemeizhan (S08S/YMZ), and Quan 9311A/YHSM (Q9311A/YHSM) represent promising new combinations with a higher specific combining ability (SCA) effect value on YPP with a value more than 3.50. Our research thus highlights the promising application for the rational utilization of YNSM and YHSM in hybrid rice breeding.
Collapse
Affiliation(s)
- Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Haoxiang Wu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhiqiang Fang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| |
Collapse
|
3
|
Long W, Li Y, Yuan Z, Luo L, Luo L, Xu W, Cai Y, Xie H. Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. PLoS One 2022; 17:e0274418. [PMID: 36215240 PMCID: PMC9550083 DOI: 10.1371/journal.pone.0274418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study, the length of insertions/deletions variation greater larger than 10 bp from 10 Oryza sativa ssp. indica rice and 10 Oryza sativa ssp. tropical japonica rice were extracted by using the Nipponbare genome as a reference. A total of 118 primer pairs which were almost evenly distributed on each chromosome corresponding to the loci of InDels were designed by the Primer 5 program. We confirmed 85 InDel markers from 60 rice varieties, including indica and tropical japonica, by running polyacrylamide gels. The InDel markers function like SSRs in identifying hybrids, calculating genetic distance, constructing the genetic linkage map, and gene mining. The InDel markers developed in this study might help in genetic studies and to investigate the tropical japonica rice varieties.
Collapse
Affiliation(s)
- Weixiong Long
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Yonghui Li
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Zhengqing Yuan
- State key Laboratory of Hybrid Rice, Wuhan University, Wuhan, China
| | - Lihua Luo
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Laiyang Luo
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Weibiao Xu
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang, China,* E-mail:
| |
Collapse
|
4
|
Kong W, Deng X, Yang J, Zhang C, Sun T, Ji W, Zhong H, Fu X, Li Y. High-resolution bin-based linkage mapping uncovers the genetic architecture and heterosis-related loci of plant height in indica-japonica derived populations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:814-827. [PMID: 35165965 DOI: 10.1111/tpj.15705] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH-related genes must be urgently identified to facilitate ideal plant architecture breeding in rice (Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis-related loci of PH in rice, we developed a high-generation (>F15 ) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA [indica] and Z7A [japonica]). Using deep resequencing data, a high-density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH-related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment-specific PH QTLs were stably detected in Hainan (qPH-3.1) or Hubei (qPH-5.1), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine-mapped, and the candidate genes qPH-3.1 and qPH-5.1 for PH were further validated using CRISPR-Cas9 gene editing. Specifically, qPH-3.1 was characterized as a pleiotropic gene, and the qPH-3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis-related QTLs were identified in the testcross populations, and a better-parent heterosis locus (qBPH-5.2) completely covered qPH-5.1. Furthermore, the cross results of fixed-genotype RILs verified the dominant effects of qPH-3.1 and qPH-5.1. Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future.
Collapse
Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wenjie Ji
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hua Zhong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| |
Collapse
|
5
|
Liu X, Hu X, Li K, Liu Z, Wu Y, Feng G, Huang C, Wang H. Identifying quantitative trait loci for the general combining ability of yield-relevant traits in maize. BREEDING SCIENCE 2021; 71:217-228. [PMID: 34377070 PMCID: PMC8329886 DOI: 10.1270/jsbbs.20008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 12/14/2020] [Indexed: 06/13/2023]
Abstract
Maize is the most important staple crop worldwide. Many of its agronomic traits present with a high level of heterosis. Combining ability was proposed to exploit the rule of heterosis, and general combining ability (GCA) is a crucial measure of parental performance. In this study, a recombinant inbred line population was used to construct testcross populations by crossing with four testers based on North Carolina design II. Six yield-relevant traits were investigated as phenotypic data. GCA effects were estimated for three scenarios based on the heterotic group and the number of tester lines. These estimates were then used to identify quantitative trait loci (QTL) and dissect genetic basis of GCA. A higher heritability of GCA was obtained for each trait. Thus, testing in early generation of breeding may effectively select candidate lines with relatively superior GCA performance. The GCA QTL detected in each scenario was slightly different according to the linkage mapping. Most of the GCA-relevant loci were simultaneously detected in all three datasets. Therefore, the genetic basis of GCA was nearly constant although discrepant inbred lines were appointed as testers. In addition, favorable alleles corresponding to GCA could be pyramided via marker-assisted selection and made available for maize hybrid breeding.
Collapse
Affiliation(s)
- Xiaogang Liu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaojiao Hu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kun Li
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhifang Liu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yujin Wu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guang Feng
- Liaoning Dandong Academy of Agricultural Sciences, Dandong 118109, China
| | - Changling Huang
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwu Wang
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
6
|
Geng X, Sun G, Qu Y, Sarfraz Z, Jia Y, He S, Pan Z, Sun J, Iqbal MS, Wang Q, Qin H, Liu J, Liu H, Yang J, Ma Z, Xu D, Yang J, Zhang J, Li Z, Cai Z, Zhang X, Zhang X, Zhou G, Li L, Zhu H, Wang L, Pang B, Du X. Genome-wide dissection of hybridization for fiber quality- and yield-related traits in upland cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1285-1300. [PMID: 32996179 PMCID: PMC7756405 DOI: 10.1111/tpj.14999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 07/14/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
An evaluation of combining ability can facilitate the selection of suitable parents and superior F1 hybrids for hybrid cotton breeding, although the molecular genetic basis of combining ability has not been fully characterized. In the present study, 282 female parents were crossed with four male parents in accordance with the North Carolina II mating scheme to generate 1128 hybrids. The parental lines were genotyped based on restriction site-associated DNA sequencing and 306 814 filtered single nucleotide polymorphisms were used for genome-wide association analysis involving the phenotypes, general combining ability (GCA) values, and specific combining ability values of eight fiber quality- and yield-related traits. The main results were: (i) all parents could be clustered into five subgroups based on population structure analyses and the GCA performance of the female parents had significant differences between subgroups; (ii) 20 accessions with a top 5% GCA value for more than one trait were identified as elite parents for hybrid cotton breeding; (iii) 120 significant single nucleotide polymorphisms, clustered into 66 quantitative trait loci, such as the previously reported Gh_A07G1769 and GhHOX3 genes, were found to be significantly associated with GCA; and (iv) identified quantitative trait loci for GCA had a cumulative effect on GCA of the accessions. Overall, our results suggest that pyramiding the favorable loci for GCA may improve the efficiency of hybrid cotton breeding.
Collapse
Affiliation(s)
- Xiaoli Geng
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhou455001China
| | - Gaofei Sun
- Anyang Institute of TechnologyAnyang455000China
| | - Yujie Qu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
| | - Zareen Sarfraz
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
| | - Yinhua Jia
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhou455001China
| | - Shoupu He
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhou455001China
| | - Zhaoe Pan
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
| | - Junling Sun
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
| | - Muhammad S. Iqbal
- Cotton Research StationAyub Agricultural Research InstituteFaisalabad38000Pakistan
| | - Qinglian Wang
- Henan Institute of Science and TechnologyXinxiang453003China
| | - Hongde Qin
- Cash Crop InstituteHubei Academy of Agricultural SciencesWuhan430000China
| | - Jinhai Liu
- Zhongmian Cotton Seed Industry Technology Co., LtdZhengzhou455001China
| | - Hui Liu
- Jing Hua Seed Industry Technologies IncJingzhou434000China
| | - Jun Yang
- Cotton Research Institute of Jiangxi ProvinceJiujiang332000China
| | - Zhiying Ma
- Key Laboratory of Crop Germplasm Resources of HebeiHebei Agricultural UniversityBaoding071000China
| | - Dongyong Xu
- Guoxin Rural Technical Service AssociationHejian062450China
| | - Jinlong Yang
- Zhongmian Cotton Seed Industry Technology Co., LtdZhengzhou455001China
| | | | - Zhikun Li
- Key Laboratory of Crop Germplasm Resources of HebeiHebei Agricultural UniversityBaoding071000China
| | - Zhongmin Cai
- Zhongmian Cotton Seed Industry Technology Co., LtdZhengzhou455001China
| | - Xuelin Zhang
- Hunan Cotton Research InstituteChangde415000China
| | - Xin Zhang
- Henan Institute of Science and TechnologyXinxiang453003China
| | - Guanyin Zhou
- Zhongmian Cotton Seed Industry Technology Co., LtdZhengzhou455001China
| | - Lin Li
- Zhongli Company of ShandongDongying257000China
| | - Haiyong Zhu
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
| | - Liru Wang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
| | - Baoyin Pang
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
| | - Xiongming Du
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyang455000China
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologyZhengzhou UniversityZhengzhou455001China
| |
Collapse
|
7
|
Lu X, Zhou Z, Yuan Z, Zhang C, Hao Z, Wang Z, Li M, Zhang D, Yong H, Han J, Li X, Weng J. Genetic Dissection of the General Combining Ability of Yield-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2020; 11:788. [PMID: 32793248 PMCID: PMC7387702 DOI: 10.3389/fpls.2020.00788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/18/2020] [Indexed: 05/27/2023]
Abstract
Maize yield components including row number, kernel number per row, kernel thickness, kernel width, kernel length, 100-kernel weight, and volume weight affect grain yield directly. Previous studies mainly focused on dissecting the genetic basis of per se performances for yield-related traits, but the genetic basis of general combining ability (GCA) for these traits is still unclear. In the present study, 328 RILs were crossed as males to two testers according to the NCII mating design, resulting in a hybrid panel composed of 656 hybrids. Both the hybrids and parental lines were evaluated in four environments in 2015 and 2016. Correlation analysis showed the performances of GCA effects were significantly correlated to the per se performances of RILs for all yield-related traits (0.17 ≤ r ≤ 0.64, P > 0.01). Only 17 of 95 QTL could be detected for both per se performances of RILs and GCA effects for eight yield-related traits. The QTL qKN7-1 and qHKW1-3, which could explain more than 10% of the variation in the GCA effects of KN and HKW, were also detected for per se performances for the traits. The pleiotropic loci qRN3-1 and qRN6, which together explained 14.92% of the observed variation in GCA effects for RN, were associated with the GCA effects of KW and HKW, but not with per se performances for these traits. In contrast, Incw1, which was related to seed weight in maize, was mapped to the region surrounding MK2567 at the qHKW5-2 locus, but no GCA effect was detected. The QTL identified in present study for per se performances and corresponding GCA effects for yield-related traits might be useful for maize hybrid breeding.
Collapse
Affiliation(s)
- Xin Lu
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaohui Yuan
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Chaoshu Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenhua Wang
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhai Li
- College of Agriculture, Northeast Agricultural University, Harbin, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
8
|
Chen J, Zhou H, Xie W, Xia D, Gao G, Zhang Q, Wang G, Lian X, Xiao J, He Y. Genome-wide association analyses reveal the genetic basis of combining ability in rice. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2211-2222. [PMID: 31004558 PMCID: PMC6790367 DOI: 10.1111/pbi.13134] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 05/12/2023]
Abstract
Combining ability is a measure for selecting elite parents and predicting hybrid performance in plant breeding. However, the genetic basis of combining ability remains unclear and a global view of combining ability from diverse mating designs is lacking. We developed a North Carolina II (NCII) population of 96 Oryza sativa and four male sterile lines to identify parents of greatest value for hybrid rice production. Statistical analyses indicated that general combining ability (GCA) and specific combining ability (SCA) contributed variously to different agronomic traits. In a genome-wide association study (GWAS) of agronomic traits, GCA and SCA, we identified 34 significant associations (P < 2.39 × 10-7 ). The superior alleles of GCA loci (Ghd8, GS3 and qSSR4) accumulated in parental lines with high GCA and explained 30.03% of GCA variance in grain yield, indicating that molecular breeding of high GCA parental lines is feasible. The distinct distributions of these QTLs contributed to the differentiation of parental GCA in subpopulations. GWAS of SCA identified 12 more loci that showed dominance on corresponding agronomic traits. We conclude that the accumulation of superior GCA and SCA alleles is an important contributor to heterosis and QTLs that greatly contributed to combining ability in our study would accelerate the identification of elite inbred lines and breeding of super hybrids.
Collapse
Affiliation(s)
- Junxiao Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanChina
| |
Collapse
|
9
|
Late flowering in F 1 hybrid rice brought about by the complementary effect of quantitative trait loci. Genetica 2019; 147:351-358. [PMID: 31432314 DOI: 10.1007/s10709-019-00075-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
Late flowering sometimes occurs in F1 hybrids between rice varieties (Oryza sativa L.), although the parental varieties show similar days-to-flowering (DTF). The genetic architecture prompting the occurrence of such late flowering is poorly understood. To clarify the genetic architecture of late flowering in F1 hybrids from a cross between rice varieties, 'Koshihikari' and 'IR64', we performed quantitative trait locus (QTL) analysis using an F2 population (selfed progeny of an F1 plant), in which heterozygous genotypes should segregate in a certain proportion in a Mendelian manner. The QTL analysis detected three significant QTLs. At one QTL (putatively Heading date 1), the 'Koshihikari' allele increased DTF, and at the other two QTLs (putatively Heading date 6 and Oryza sativa Pseudo-Response Regulator 37/Heading date 2), the 'IR64' alleles increased DTF. All alleles at these three QTLs showed partial dominance. The combination of the QTLs explained 82.2% of the total phenotypic variance of DTF in the F2 population, with contribution from epistasis between QTLs. There was no difference between DTFs of F1 hybrids and heterozygous genotypes for the three QTLs. Our results demonstrated that the complementary effects accompanied by epistasis of at least three QTLs were responsible for late flowering in F1 hybrids.
Collapse
|
10
|
Fan F, Long W, Liu M, Yuan H, Pan G, Li N, Li S. Quantitative Trait Locus Mapping of the Combining Ability for Yield-Related Traits in Wild Rice Oryza longistaminata. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8766-8772. [PMID: 31313921 DOI: 10.1021/acs.jafc.9b02224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In decades of hybrid rice breeding, the combining ability has been successfully used to evaluate excellent parental lines and predict heterosis. However, previous studies for the combining ability mainly focused on cultivated rice and rarely involved wild rice. In this study, for the first time, we identified 20 new quantitative trait loci (QTLs) for the combining ability in wild rice using a North Carolina II mating design. Among them, qGCA1, one of the major QTLs that can significantly improve the general combining ability of the plant height, spikelet number, and yield per plant, was delimited to an interval of about 72 kb on chromosome 1. qSCA8, another major QTL, which can significantly improve the specific combining ability of the seed-setting rate and yield per plant, was located in an interval of about 90 kb on chromosome 8. These QTLs discovered from wild rice will provide new ideas to explain the genetic mechanism of the combining ability and establish the basis for breeding of high-combining-ability rice.
Collapse
Affiliation(s)
- Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| | - Weixiong Long
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| | - Manman Liu
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| | - Guojing Pan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| | - Nengwu Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science , Wuhan University , Wuhan , Hubei 430072 , People's Republic of China
| |
Collapse
|