1
|
|
2
|
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
|
3
|
Chen X, Zhao B, Ji C, Zhu B, Wang R. Transcriptome profiling analysis of two contrasting barley genotypes in general combining ability for yield traits. BRAZILIAN JOURNAL OF BOTANY 2021; 44:117-123. [DOI: 10.1007/s40415-020-00696-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 09/01/2023]
|
4
|
Mahmood T, Wang X, Ahmar S, Abdullah M, Iqbal MS, Rana RM, Yasir M, Khalid S, Javed T, Mora-Poblete F, Chen JT, Shah MKN, Du X. Genetic Potential and Inheritance Pattern of Phenological Growth and Drought Tolerance in Cotton ( Gossypium Hirsutum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:705392. [PMID: 34630456 PMCID: PMC8497812 DOI: 10.3389/fpls.2021.705392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/23/2021] [Indexed: 05/22/2023]
Abstract
Cotton has prime importance in the global economy and governs socio-economic affairs of the world. Water scarcity and high temperature are major constraints that badly affect cotton production, which shows the need for the development of drought-tolerant varieties. Ten cotton genotypes, including three drought-tolerant and seven susceptible, were identified from a panel of diverse cotton genotypes at the seedling stage under two contrasting water regimes. Three lines were crossed with seven testers under line × tester mating design. The 21 F1 cross combinations along with 10 parents were evaluated under 100% non-stress (NS) and 50% drought stress (DS) filed capacity to assess the effects of drought stress and its inheritance in the next generation. All the genotypes were evaluated till the maturity stage for combining ability, heritability, and other genetic factors to understand the drought tolerance mechanisms. The proportional contribution of lines in the total variance evidenced that lines had a significant higher contribution in total variance for days to boll opening (DBO) of 10% and proline contents (PC) of 13% under DS conditions. It indicates that lines contributed more positive alleles for such traits. Under DS condition, DTV-9 × BT-252 and DTV-9 × DTV-10 had maximum negative specific combining ability (SCA) effects for DBO. Simultaneously, DBO also had higher heritability (h2) which indicates its dominant gene action and meanwhile, the importance of these combinations for the early mature and short duration variety development. The results revealed that most of the studied traits, including days taken to maturity, yield traits, and physiological traits, are under significant genetic control, with a strong genetic basis and have a huge potential for improving drought tolerance in cotton. Drought tolerance was found to have a strong association with early maturity and agro-climatic conditions of the cultivated areas. Identified superior parents in this study are suggested to use in the future breeding program to advance the cotton growth and drought tolerance.
Collapse
Affiliation(s)
- Tahir Mahmood
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, China
- Xiukang Wang
| | - Sunny Ahmar
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Abdullah
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Shahid Iqbal
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Rashid Mehmood Rana
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Yasir
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Shiguftah Khalid
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Talha Javed
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Muhammad Kausar Nawaz Shah
- Department of Plant Breeding and Genetics, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Xiongming Du
| |
Collapse
|
5
|
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
|
6
|
Shi Y, Liu A, Li J, Zhang J, Li S, Zhang J, Ma L, He R, Song W, Guo L, Lu Q, Xiang X, Gong W, Gong J, Ge Q, Shang H, Deng X, Pan J, Yuan Y. Examining two sets of introgression lines across multiple environments reveals background-independent and stably expressed quantitative trait loci of fiber quality in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2075-2093. [PMID: 32185421 PMCID: PMC7311500 DOI: 10.1007/s00122-020-03578-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/07/2020] [Indexed: 05/29/2023]
Abstract
Background-independent (BI) and stably expressed (SE) quantitative trait loci (QTLs) were identified using two sets of introgression lines across multiple environments. Genetic background more greatly affected fiber quality traits than environmental factors. Sixty-one SE-QTLs, including two BI-QTLs, were novel and 48 SE-QTLs, including seven BI-QTLs, were previously reported. Cotton fiber quality traits are controlled by QTLs and are susceptible to environmental influence. Fiber quality improvement is an essential goal in cotton breeding but is hindered by limited knowledge of the genetic basis of fiber quality traits. In this study, two sets of introgression lines of Gossypium hirsutum × G. barbadense were used to dissect the QTL stability of three fiber quality traits (fiber length, strength and micronaire) across environments using 551 simple sequence repeat markers selected from our high-density genetic map. A total of 76 and 120 QTLs were detected in the CCRI36 and CCRI45 backgrounds, respectively. Nine BI-QTLs were found, and 78 (41.71%) of the detected QTLs were reported previously. Thirty-nine and 79 QTLs were SE-QTLs in at least two environments in the CCRI36 and CCRI45 backgrounds, respectively. Forty-eight SE-QTLs, including seven BI-QTLs, were confirmed in previous reports, and 61 SE-QTLs, including two BI-QTLs, were considered novel. These results indicate that genetic background more strongly impacts on fiber quality traits than environmental factors. Twenty-three clusters with BI- and/or SE-QTLs were identified, 19 of which harbored favorable alleles from G. barbadense for two or three fiber quality traits. This study is the first report using two sets of introgression lines to identify fiber quality QTLs across environments in cotton, providing insights into the effect of genetic backgrounds and environments on the QTL expression of fiber quality and important information for the genetic basis underlying fiber quality traits toward QTL cloning and molecular breeding.
Collapse
Affiliation(s)
- Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Shaoqi Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jinfeng Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liujun Ma
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Rui He
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Weiwu Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lixue Guo
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Quanwei Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xianghui Xiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| |
Collapse
|
7
|
Eltahawy MS, Ali N, Zaid IU, Li D, Abdulmajid D, Bux L, Wang H, Hong D. Association analysis between constructed SNPLDBs and GCA effects of 9 quality-related traits in parents of hybrid rice (Oryza sativa L.). BMC Genomics 2020; 21:31. [PMID: 31918652 PMCID: PMC6953305 DOI: 10.1186/s12864-019-6428-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 12/24/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The general combining ability (GCA) of parents in hybrid rice affects not only heterotic level of grain yield and other important agronomic traits, but also performance of grain quality traits of F2 bulk population which is the commodity consumed by humans. In order to make GCA improvement for quality traits in parents of hybrid rice by molecular marker assisted selection feasible, genome-wide GCA loci for quality traits in parents were detected through association analysis between the effects of GCA and constructed single nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs), by using unhusked rice grains harvested from F1 plants of 48 crosses of Indica rice and 78 crosses of Japonica rice. GCA-SNPLDBs association analysis. RESULTS Among the 8 CMS and 6 restorer lines of indica rice subspecies, CMS lines Zhenpin A, Zhenshan97 A, and 257A, and restorers Kanghui98, Minghui63 and Yanhui559 were recognized as good general combiners based on their GCA effect values for the 9 quality traits (brown rice rate, milled rice rate, head rice rate, percentage of chalky grains, chalky area size, chalkiness degree, gelatinization temperature, gel consistency and amylose content). Among the 13 CMS and 6 restorer lines of japonica rice subspecies, CMS 863A, 6427A and Xu 2A, and restorers C418, Ninghui8hao and Yunhui4hao showed elite GCA effect values for the 9 traits. GCA-SNPLDB association analysis revealed 39 significant SNPLDB loci associated with the GCA of the 9 quality-related traits, and the numbers of SNPLDB loci located on chromosome 1, 2, 3, 4, 5, 8, 9, 11 and 12 were 1, 4, 3, 9, 6, 5, 5, 4 and 2, respectively. Number of superior GCA alleles for the 9 traits among the 33 parents ranged from 1 to 26. CONCLUSIONS Thirty-nine significant SNPLDBs loci were identified associated with the GCA of 9 quality-related traits, and the superior SNPLDB alleles could be used to improve the GCA of parents for the traits in the future by molecular marker assisted selection. The genetic basis of trait GCA in parents is different from that of trait itself.
Collapse
Affiliation(s)
- Moaz S Eltahawy
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Agronomy Department, Faculty of Agriculture, Zagazig University, Sharqia, 44519, Egypt
| | - Nour Ali
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Laboratory of Crop Genetics and Germplasm Enhancement, Field Crops Research Department, Agricultural Faculty, Damascus University, Damascus, Syria
| | - Imdad U Zaid
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dalu Li
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dina Abdulmajid
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.,Rice Research and Training Centre, Field Crops Research Institute, Agricultural Research Centre, Kafr El-Sheikh, 33717, Egypt
| | - Lal Bux
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Wang
- Nanjing Agricultural University, Nanjing, 210095, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Delin Hong
- Nanjing Agricultural University, Nanjing, 210095, China. .,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, 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
|
Basava RK, Hash CT, Mahendrakar MD, Kishor P. B. K, Satyavathi CT, Kumar S, Singh RB, Yadav RS, Gupta R, Srivastava RK. Discerning combining ability loci for divergent environments using chromosome segment substitution lines (CSSLs) in pearl millet. PLoS One 2019; 14:e0218916. [PMID: 31461465 PMCID: PMC6713397 DOI: 10.1371/journal.pone.0218916] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022] Open
Abstract
Pearl millet is an important crop for arid and semi-arid regions of the world. Genomic regions associated with combining ability for yield-related traits under irrigated and drought conditions are useful in heterosis breeding programs. Chromosome segment substitution lines (CSSLs) are excellent genetic resources for precise QTL mapping and identifying naturally occurring favorable alleles. In the present study, testcross hybrid populations of 85 CSSLs were evaluated for 15 grain and stover yield-related traits for summer and wet seasons under irrigated control (CN) and moisture stress (MS) conditions. General combining ability (GCA) and specific combining ability (SCA) effects of all these traits were estimated and significant marker loci linked to GCA and SCA of the traits were identified. Heritability of the traits ranged from 53-94% in CN and 63-94% in MS. A total of 40 significant GCA loci and 36 significant SCA loci were identified for 14 different traits. Five QTLs (flowering time, panicle number and panicle yield linked to Xpsmp716 on LG4, flowering time and grain number per panicle with Xpsmp2076 on LG4) simultaneously controlled both GCA and SCA, demonstrating their unique genetic basis and usefulness for hybrid breeding programs. This study for the first time demonstrated the potential of a set of CSSLs for trait mapping in pearl millet. The novel combining ability loci linked with GCA and SCA values of the traits identified in this study may be useful in pearl millet hybrid and population improvement programs using marker-assisted selection (MAS).
Collapse
Affiliation(s)
- Ramana Kumari Basava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | - Charles Thomas Hash
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | - Mahesh D. Mahendrakar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | | | - C. Tara Satyavathi
- All India Coordinated Research Project on Pearl Millet (AICRP-PM), Indian Council of Agricultural Research (ICAR), Mandor, Jodhpur, Rajasthan, India
| | - Sushil Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
- Anand Agricultural University, Anand, Gujarat, India
| | - R. B. Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | - Rattan S. Yadav
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Wales, United Kingdom
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana State, India
| |
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
|
11
|
Dissecting Heterosis During the Ear Inflorescence Development Stage in Maize via a Metabolomics-based Analysis. Sci Rep 2019; 9:212. [PMID: 30659214 PMCID: PMC6338801 DOI: 10.1038/s41598-018-36446-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/13/2018] [Indexed: 11/08/2022] Open
Abstract
Heterosis can increase the yield of many crops and has been extensively applied in agriculture. In maize, female inflorescence architecture directly determines grain yield. Thus, exploring the relationship between early maize ear inflorescence development and heterosis regarding yield-related traits may be helpful for characterizing the molecular mechanisms underlying heterotic performance. In this study, we fine mapped the overdominant heterotic locus (hlEW2b), associated with ear width, in an approximately 1.98-Mb region based on analyses of chromosome segment substitution lines and the corresponding testcross population. Maize ear inflorescences at the floral meristem stage were collected from two inbred lines, one chromosome segment substitution line that carried hlEW2b (sub-CSSL16), the receptor parent lx9801, and the Zheng58 × sub-CSSL16 and Zheng58 × lx9801 hybrid lines. A total of 256 metabolites were identified, including 31 and 24 metabolites that were differentially accumulated between the two hybrid lines and between the two inbred lines, respectively. Most of these metabolites are involved in complex regulatory mechanisms important for maize ear development. For example, nucleotides are basic metabolites affecting cell composition and carbohydrate synthesis. Additionally, nicotinate and nicotinamide metabolism is important for photosynthesis, plant stress responses, and cell expansion. Moreover, flavonoid and phenolic metabolites regulate auxin transport and cell apoptosis. Meanwhile, phytohormone biosynthesis and distribution influence the cell cycle and cell proliferation. Our results revealed that changes in metabolite contents may affect the heterotic performance related to ear width and yield in maize hybrid lines. This study provides new clues in heterosis at the metabolomics level and implies that differentially accumulated metabolites made distinct contributions to the heterosis at an early stage of ear inflorescences development.
Collapse
|
12
|
Zhou Z, Zhang C, Lu X, Wang L, Hao Z, Li M, Zhang D, Yong H, Zhu H, Weng J, Li X. Dissecting the Genetic Basis Underlying Combining Ability of Plant Height Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:1117. [PMID: 30116252 PMCID: PMC6083371 DOI: 10.3389/fpls.2018.01117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 07/11/2018] [Indexed: 05/27/2023]
Abstract
Maize plant height related traits including plant height, ear height, and internode number are tightly linked with biomass, planting density, and grain yield in the field. Previous studies have focused on understanding the genetic basis of plant architecture traits per se, but the genetic basis of combining ability remains poorly understood. In this study, 328 recombinant inbred lines were inter-group crossed with two testers to produce 656 hybrids using the North Carolina II mating design. Both of the parental lines and hybrids were evaluated in two summer maize-growing regions of China in 2015 and 2016. QTL mapping highlighted that 7 out of 16 QTL detected for RILs per se could be simultaneously detected for general combining ability (GCA) effects, suggesting that GCA effects and the traits were genetically controlled by different sets of loci. Among the 35 QTL identified for hybrid performance, 57.1% and 28.5% QTL overlapped with additive/GCA and non-additive/SCA effects, suggesting that the small percentage of hybrid variance due to SCA effects in our design. Two QTL hotspots, located on chromosomes 5 and 10 and including the qPH5-1 and qPH10 loci, were validated for plant height related traits by Ye478 derivatives. Notably, the qPH5-1 locus could simultaneously affect the RILs per se and GCA effects while the qPH10, a major QTL (PVE > 10%) with pleiotropic effects, only affected the GCA effects. These results provide evidence that more attention should be focused on loci that influence combining ability directly in maize hybrid breeding.
Collapse
Affiliation(s)
- Zhiqiang Zhou
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaoshu Zhang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohuan Lu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Zhuanfang Hao
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hanyong Zhu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Yunnan Wenshanzhou Academy of Agricultural Sciences, Wenshan, China
| | - Jianfeng Weng
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhai Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
13
|
Wang Y, Zhang X, Shi X, Sun C, Jin J, Tian R, Wei X, Xie H, Guo Z, Tang J. Heterotic loci identified for maize kernel traits in two chromosome segment substitution line test populations. Sci Rep 2018; 8:11101. [PMID: 30038303 PMCID: PMC6056474 DOI: 10.1038/s41598-018-29338-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 07/10/2018] [Indexed: 01/19/2023] Open
Abstract
Heterosis has been widely used to increase grain quality and yield, but its genetic mechanism remains unclear. In this study, the genetic basis of heterosis for four maize kernel traits was examined in two test populations constructed using a set of 184 chromosome segment substitution lines (CSSLs) and two inbred lines (Zheng58 and Xun9058) in two environments. 63 and 57 different heterotic loci (HL) were identified for four kernel traits in the CSSLs × Zheng58 and CSSLs × Xun9058 populations, respectively. Of these, nine HL and six HL were identified for four kernel traits in the CSSLs × Zheng58 and CSSLs × Xun9058 populations, at the two locations simultaneously. Comparative analysis of the HL for the four kernel traits identified only 21 HL in the two test populations simultaneously. These results showed that most HL for the four kernel traits differed between the two test populations. The common HL were important loci from the Reid × Tangsipingtou heterotic model, and could be used to predict hybrid performance in maize breeding.
Collapse
Affiliation(s)
- Yafei Wang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiangge Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
- Agronomy College, Sichuan Agricultural University, Wenjiang, 611130, China
| | - Xia Shi
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Canran Sun
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiao Jin
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Runmiao Tian
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoyi Wei
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453003, China
| | - Huiling Xie
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450002, China.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025, China.
| |
Collapse
|
14
|
Zhou H, Xia D, Zeng J, Jiang G, He Y. Dissecting combining ability effect in a rice NCII-III population provides insights into heterosis in indica-japonica cross. RICE (NEW YORK, N.Y.) 2017; 10:39. [PMID: 28853048 PMCID: PMC5574824 DOI: 10.1186/s12284-017-0179-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 08/21/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Combining ability is a measure for selecting elite parents that make the highest contributions to hybrid performance. However, the genetic bases of combining ability and how they contributed to heterosis is seldomly known. RESULTS We constructed a both NCII and NCIII population derived from an indica-japonica cross to study the relationship among parental performance, combining ability and hybrid performance of 11 agronomic traits. Among them, specific combining ability is more important to grain yield than parental performance and general combining ability. We performed linkage analyses to phenotypic values and combining ability of all 11 traits in Doubled haploid lines and its two backcross populations and identified 108 QTLs in total. Among these QTLs, four known loci, Sd1, Ghd7, Ghd8 and DEP1 contribute a lot to GCA effects of agronomic traits except grain yield and seed setting rate. Three QTLs, Ghd8, S5 and qS12, contribute a lot to SCA effects of grain yield and present overdominace. CONCLUSIONS Our study provides insights into the genetic bases of combining ability and heterosis and will promote the improvements of indica-japonica hybrid breeding.
Collapse
Affiliation(s)
- Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Jing Zeng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Gonghao Jiang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
15
|
Yan J, Wu Y, Li W, Qin X, Wang Y, Yue B. Genetic mapping with testcrossing associations and F 2:3 populations reveals the importance of heterosis in chilling tolerance at maize seedling stage. Sci Rep 2017; 7:3232. [PMID: 28607429 PMCID: PMC5468334 DOI: 10.1038/s41598-017-03585-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/02/2017] [Indexed: 11/09/2022] Open
Abstract
Maize seedlings are sensitive to low temperatures, and genetic mapping for chilling tolerance at the seedling stage with genetically diverse populations would facilitate the genetic improvement of this important trait. In this study, quantitative trait loci (QTL) mapping for four chilling tolerance-related traits at the seedling stage was conducted via a genome-wide association study (GWAS) with 338 testcrosses. A total of 32 significant loci and 36 stress tolerance-related candidate genes were identified, though none of them have been revealed by QTL mapping using maize inbred lines in previous reports. Moreover, expression of ten of the candidate genes was induced by chilling stress in a maize hybrid, though only a few of these genes were upregulated in its tolerant parent. These implied that heterosis might be involved in maize chilling tolerance. To further evaluate the importance of heterosis in chilling tolerance at the seedling stage, genetic mapping for chilling tolerance was conducted using an F2:3 population derived from the two inbred lines used for the gene expression assay. Of the seven QTL revealed, six loci showed partial dominance or over-dominance effects. Results from this study demonstrate that heterosis plays an important role in chilling tolerance in maize seedlings.
Collapse
Affiliation(s)
- Jinbo Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yu Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wenming Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiner Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yi Wang
- Industrial Crops Research Institution, Heilongjiang Academy of Land Reclamation of Sciences, Haerbin, China
| | - Bing Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
| |
Collapse
|
16
|
Ertiro BT, Beyene Y, Das B, Mugo S, Olsen M, Oikeh S, Juma C, Labuschagne M, Prasanna BM. Combining ability and testcross performance of drought-tolerant maize inbred lines under stress and non-stress environments in Kenya. PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2017; 136:197-205. [PMID: 28781399 PMCID: PMC5518761 DOI: 10.1111/pbr.12464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 01/04/2017] [Indexed: 05/24/2023]
Abstract
Drought and poor soil fertility are among the major abiotic stresses affecting maize productivity in sub-Saharan Africa. Maize breeding efforts at the International Maize and Wheat Improvement Center (CIMMYT) have focused on incorporating drought stress tolerance and nitrogen-use efficiency (NUE) into tropical maize germplasm. The objectives of this study were to estimate the general combining ability (GCA) and specific combining ability (SCA) of selected maize inbred lines under drought stress (DS), low-nitrogen (LN) and optimum moisture and nitrogen (optimum) conditions, and to assess the yield potential and stability of experimental hybrids under these management conditions. Forty-nine experimental three-way cross hybrids, generated from a 7 × 7 line by tester crosses, and six commercial checks were evaluated across 11 optimum, DS and LN sites in Kenya in 2014 using an alpha lattice design with two replicates per entry at each site. DS reduced both grain yield (GY) and plant height (PH), while anthesis-silking interval (ASI) increased under both DS and LN. Hybrids 'L4/T2' and 'L4/T1' were found to be superior and stable, while inbreds 'L4' and 'L6' were good combiners for GY and other secondary traits across sites. Additive variance played a greater role for most traits under the three management conditions, suggesting that further progress in the improvement of these traits should be possible. GY under optimum conditions was positively correlated with GY under both DS and LN conditions, but GY under DS and LN was not correlated. Our results suggest the feasibility for simultaneous improvement in grain yield performance of genotypes under optimum, DS and LN conditions.
Collapse
Affiliation(s)
- Berhanu T. Ertiro
- Ethiopian Institute of Agricultural Research (EIAR)Bako National Maize Research CenterP.O.Box 03BakoWest ShoaOromiaEthiopia
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Stephen Mugo
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Sylvester Oikeh
- African Agricultural Technology Foundation (AATF)P.O. Box 30709‐00100NairobiKenya
| | - Collins Juma
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Maryke Labuschagne
- Department of Plant SciencesUniversity of the Free StateP.O. Box 339Bloemfontein9300Republic of South Africa
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| |
Collapse
|
17
|
Luo X, Ding Y, Zhang L, Yue Y, Snyder JH, Ma C, Zhu J. Genomic Prediction of Genotypic Effects with Epistasis and Environment Interactions for Yield-Related Traits of Rapeseed ( Brassica napus L.). Front Genet 2017; 8:15. [PMID: 28270831 PMCID: PMC5318398 DOI: 10.3389/fgene.2017.00015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 02/03/2017] [Indexed: 11/16/2022] Open
Abstract
Oilseed rape (Brassica napus) is an economically important oil crop, yet the genetic architecture of its complex traits remain largely unknown. Here, genome-wide association study was conducted for eight yield-related traits to dissect the genetic architecture of additive, dominance, epistasis, and their environment interaction. Additionally, the optimal genotype combination and the breeding value of superior line, superior hybrid and existing best line in mapping population were predicted for each trait in two environments based on the predicted genotypic effects. As a result, 17 quantitative trait SNPs (QTSs) were identified significantly for target traits with total heritability varied from 58.47 to 87.98%, most of which were contributed by dominance, epistasis, and environment-specific effects. The results indicated that non-additive effects were large contributions to heritability and epistasis, and also noted that environment interactions were important variants for oilseed breeding. Our study facilitates the understanding of genetic basis of rapeseed yield trait, helps to accelerate rapeseed breading, and also offers a roadmap for precision plant breeding via marker-assisted selection.
Collapse
Affiliation(s)
- Xiang Luo
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University Wuhan, China
| | - Yi Ding
- Institute of Bioinformatics, Zhejiang University Hangzhou, China
| | - Linzhong Zhang
- Economic and Technical College, Anhui Agricultural University Hefei, China
| | - Yao Yue
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University Wuhan, China
| | - John H Snyder
- Institute of Bioinformatics, Zhejiang University Hangzhou, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University Wuhan, China
| | - Jun Zhu
- Institute of Bioinformatics, Zhejiang University Hangzhou, China
| |
Collapse
|
18
|
Zaid IU, Tang W, Liu E, Khan SU, Wang H, Mawuli EW, Hong D. Genome-Wide Single-Nucleotide Polymorphisms in CMS and Restorer Lines Discovered by Genotyping Using Sequencing and Association with Marker-Combining Ability for 12 Yield-Related Traits in Oryza sativa L. subsp. Japonica. FRONTIERS IN PLANT SCIENCE 2017; 8:143. [PMID: 28228768 PMCID: PMC5297617 DOI: 10.3389/fpls.2017.00143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 01/24/2017] [Indexed: 05/26/2023]
Abstract
Heterosis or hybrid vigor is closely related with general combing ability (GCA) of parents and special combining ability (SCA) of combinations. The evaluation of GCA and SCA facilitate selection of parents and combinations in heterosis breeding. In order to improve combining ability (CA) by molecular marker assist selection, it is necessary to identify marker loci associated with the CA. To identify the single nucleotide polymorphisms (SNP) loci associated with CA in the parental genomes of japonica rice, genome-wide discovered SNP loci were tested for association with the CA of 18 parents for 12 yield-related traits. In this study, 81 hybrids were created and evaluated to calculate the CA of 18 parents. The parents were sequenced by genotyping by sequencing (GBS) method for identification of genome-wide SNPs. The analysis of GBS indicated that the successful mapping of 9.86 × 106 short reads in the Nipponbare reference genome consists of 39,001 SNPs in parental genomes at 11,085 chromosomal positions. The discovered SNPs were non-randomly distributed within and among the 12 chromosomes of rice. Overall, 20.4% (8026) of the discovered SNPs were coding types, and 8.6% (3344) and 9.9% (3951) of the SNPs revealed synonymous and non-synonymous changes, which provide valuable knowledge about the underlying performance of the parents. Furthermore, the associations between SNPs and CA indicated that 362 SNP loci were significantly related to the CA of 12 parental traits. The identified SNP loci of CA in our study were distributed genome wide and caused a positive or negative effect on the CA of traits. For the yield-related traits, such as grain thickness, days to heading, panicle length, grain length and 1000-grain weight, a maximum number of positive SNP loci of CA were found in CMS A171 and in the restorers LC64 and LR27. On an individual basis, some of associated loci that resided on chromosomes 2, 5, 7, 9, and 11 recorded maximum positive values for the CA of traits. From our results, we suggest that heterosis in japonica rice would be improved by pyramiding the favorable SNP loci of CA and eliminating the unfavorable loci from parental genomes.
Collapse
Affiliation(s)
- Imdad U. Zaid
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Weijie Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Erbao Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Sana U. Khan
- School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia
| | - Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Edzesi W. Mawuli
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
| |
Collapse
|
19
|
Xu Q, Xu X, Shi Y, Qi X, Chen X. Elucidation of the molecular responses of a cucumber segment substitution line carrying Pm5.1 and its recurrent parent triggered by powdery mildew by comparative transcriptome profiling. BMC Genomics 2017; 18:21. [PMID: 28056792 PMCID: PMC5217421 DOI: 10.1186/s12864-016-3438-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Powdery mildew (PM) is one of the most severe fungal diseases of cucurbits, but the molecular mechanisms underlying PM resistance in cucumber remain elusive. In this study, we developed a PM resistant segment substitution line SSL508-28 that carried a segment on chromosome five representing the Pm5.1 locus from PM resistant donor Jin5-508 using marker-assisted backcrossing of an elite PM susceptible cucumber inbred line D8. RESULTS Whole-genome resequencing of SSL508-28, Jin5-508 and D8 was performed to identify the exact boundaries of the breakpoints for this introgression because of the low density of available single sequence repeat markers. This led to the identification of a ~6.8 Mb substituted segment predicted to contain 856 genes. RNA-seq was used to study gene expression differences in PM treated (plants harvested 48 h after inoculation) and untreated (control) SSL508-28 and D8 lines. Exactly 1,248 and 1,325 differentially expressed genes (DEGs) were identified in SSL508-28 and D8, respectively. Of those, 88 DEGs were located in the ~6.8 Mb segment interval. Based on expression data and annotation, we identified 8 potential candidate genes that may participate in PM resistance afforded by Pm5.1, including two tandemly arrayed genes encoding receptor protein kinases, two transcription factors, two genes encoding remorin proteins, one gene encoding a P-type ATPase and one gene encoding a 70 kDa heat shock protein. The transcriptome data also revealed a complex regulatory network for Pm5.1-mediated PM resistance that may involve multiple signal regulators and transducers, cell wall modifications and the salicylic acid signaling pathway. CONCLUSION These findings shed light on the cucumber PM defense mechanisms mediated by Pm5.1 and provided valuable information for the fine mapping of Pm5.1 and breeding of cucumber with enhanced resistance to PM.
Collapse
Affiliation(s)
- Qiang Xu
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xuewen Xu
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Yang Shi
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xiaohua Qi
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| | - Xuehao Chen
- Department of horticulture, School of horticulture and plant protection, Yangzhou University, 48 east wenhui road, Yangzhou, Jiangsu 225009 China
| |
Collapse
|
20
|
Whole-Genome Resequencing of a Cucumber Chromosome Segment Substitution Line and Its Recurrent Parent to Identify Candidate Genes Governing Powdery Mildew Resistance. PLoS One 2016; 11:e0164469. [PMID: 27764118 PMCID: PMC5072683 DOI: 10.1371/journal.pone.0164469] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/26/2016] [Indexed: 11/19/2022] Open
Abstract
Cucumber is an economically important vegetable crop worldwide. Powdery mildew (PM) is one of the most severe diseases that can affect cucumber crops. There have been several research efforts to isolate PM resistance genes for breeding PM-resistant cucumber. In the present study, we used a chromosome segment substitution line, SSL508-28, which carried PM resistance genes from the donor parent, JIN5-508, through twelve generations of backcrossing with a PM-susceptible inbred line, D8. We performed whole-genome resequencing of SSL508-28 and D8 to identify single nucleotide polymorphisms (SNPs), and insertions and deletions (indels). When compared against the reference genome of the inbred cucumber line 9930, a total of 468,616 SNPs and 67,259 indels were identified in SSL508-28, and 537,352 SNPs and 91,698 indels were identified in D8. Of these, 3,014 non-synonymous SNPs and 226 frameshift indels in SSL508-28, and 3,104 non-synonymous SNPs and 251 frameshift indels in D8, were identified. Bioinformatics analysis of these variations revealed a total of 15,682 SNPs and 6,262 indels between SSL508-28 and D8, among which 120 non-synonymous SNPs and 30 frameshift indels in 94 genes were detected between SSL508-28 and D8. Finally, out of these 94 genes, five resistance genes with nucleotide-binding sites and leucine-rich repeat domains were selected for qRT-PCR analysis. This revealed an upregulation of two transcripts, Csa2M435460.1 and Csa5M579560.1, in SSL508-28. Furthermore, the results of qRT-PCR analysis of these two genes in ten PM resistant and ten PM susceptible cucumber lines showed that when exposed to PM, Csa2M435460.1 and Csa5M579560.1 exhibited a higher expression level of resistant lines than susceptible lines. This indicates that Csa2M435460.1 and Csa5M579560.1 are candidate genes for PM resistance in cucumber. In addition, the non-synonymous SNPs in Csa2M435460.1 and Csa5M579560.1, identified in SSL508-28 and D8, might be the key to high PM-resistance in SSL508-28.
Collapse
|
21
|
Breeding signature of combining ability improvement revealed by a genomic variation map from recurrent selection population in Brassica napus. Sci Rep 2016; 6:29553. [PMID: 27412721 PMCID: PMC4944167 DOI: 10.1038/srep29553] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/17/2016] [Indexed: 11/30/2022] Open
Abstract
Combining ability is crucial for parent selection in crop hybrid breeding. The present investigation and results had revealed the underlying genetic factors which might contribute in adequate combining ability, further assisting in enhancing heterosis and stability. Here, we conducted a large-scale analysis of genomic variation in order to define genomic regions affecting the combining ability in recurrent selection population of rapeseed. A population of 175 individuals was genotyped with the Brassica60K SNP chip. 525 hybrids were assembled with three different testers and used to evaluate the general combining ability (GCA) in three environments. By detecting the changes of the genomic variation, we identified 376 potential genome regions, spanning 3.03% of rapeseed genome which provided QTL-level resolution on potentially selected variants. More than 96% of these regions were located in the C subgenome, indicating that C subgenome had sustained stronger selection pressure in the breeding program than the A subgenome. In addition, a high level of linkage disequilibrium in rapeseed genome was detected, suggesting that marker-assisted selection for the population improvement might be easily implemented. This study outlines the evidence for high GCA on a genomic level and provided underlying molecular mechanism for recurrent selection improvement in B. napus.
Collapse
|
22
|
Xu X, Yu T, Xu R, Shi Y, Lin X, Xu Q, Qi X, Weng Y, Chen X. Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:507-16. [PMID: 26660669 DOI: 10.1007/s00122-015-2644-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/24/2015] [Indexed: 05/09/2023]
Abstract
A dominantly inherited major-effect QTL for powdery mildew resistance in cucumber was fine mapped. Two tandemly arrayed cysteine-rich receptor-like protein kinase genes were identified as the most possible candidates. Powdery mildew (PM) is one of the most severe fungal diseases of cucumber (Cucumis sativus L.) and other cucurbit crops, but the molecular genetic mechanisms of powdery mildew resistance in cucurbits are still poorly understood. In this study, through marker-assisted backcrossing with an elite cucumber inbred line, D8 (PM susceptible), we developed a single-segment substitution line, SSSL0.7, carrying 95 kb fragment from PM resistance donor, Jin5-508, that was defined by two microsatellite markers, SSR16472 and SSR16881. A segregating population with 3600 F2 plants was developed from the SSSL0.7 × D8 mating; segregation analysis confirmed a dominantly inherited major-effect QTL, Pm1.1 in cucumber chromosome 1 underlying PM resistance in SSSL0.7. New molecular markers were developed through exploring the next generation resequenced genomes of Jin5-508 and D8. Linkage analysis and QTL mapping in a subset of the F2 plants delimited the Pm1.1 locus into a 41.1 kb region, in which eight genes were predicted. Comparative gene expression analysis revealed that two concatenated genes, Csa1M064780 and Csa1M064790 encoding the same function of a cysteine-rich receptor-like protein kinase, were the most likely candidate genes. GFP fusion protein-aided subcellular localization indicated that both candidate genes were located in the plasma membrane, but Csa1M064780 was also found in the nucleus. This is the first report of dominantly inherited PM resistance in cucumber. Results of this study will provide new insights into understanding the phenotypic and genetic mechanisms of PM resistance in cucumber. This work should also facilitate marker-assisted selection in cucumber breeding for PM resistance.
Collapse
Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ting Yu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Ruixue Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yang Shi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiaojian Lin
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| |
Collapse
|
23
|
Liu Y, Hou X, Xiao Q, Yi Q, Bian S, Hu Y, Liu H, Zhang J, Hao X, Cheng W, Li Y, Huang Y. Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents. FRONTIERS IN PLANT SCIENCE 2016; 7:1417. [PMID: 27721817 PMCID: PMC5034680 DOI: 10.3389/fpls.2016.01417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/06/2016] [Indexed: 05/17/2023]
Abstract
The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.
Collapse
Affiliation(s)
- Yinghong Liu
- Maize Research Institute, Sichuan Agricultural UniversityChengdu, China
| | - Xianbin Hou
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Qianlin Xiao
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Qiang Yi
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Shaowei Bian
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural UniversityYa'an, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural UniversityYa'an, China
| | - Xiaoqin Hao
- College of Agronomy, Guangxi UniversityNanning, China
| | - Weidong Cheng
- Maize Research Institute, Guangxi Academy of Agricultural SciencesNanning, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Yu Li
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural UniversityChengdu, China
- Yubi Huang
| |
Collapse
|
24
|
Wen J, Zhao X, Wu G, Xiang D, Liu Q, Bu SH, Yi C, Song Q, Dunwell JM, Tu J, Zhang T, Zhang YM. Genetic dissection of heterosis using epistatic association mapping in a partial NCII mating design. Sci Rep 2015; 5:18376. [PMID: 26679476 PMCID: PMC4683666 DOI: 10.1038/srep18376] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/17/2015] [Indexed: 12/31/2022] Open
Abstract
Heterosis refers to the phenomenon in which an F1 hybrid exhibits enhanced growth or agronomic performance. However, previous theoretical studies on heterosis have been based on bi-parental segregating populations instead of F1 hybrids. To understand the genetic basis of heterosis, here we used a subset of F1 hybrids, named a partial North Carolina II design, to perform association mapping for dependent variables: original trait value, general combining ability (GCA), specific combining ability (SCA) and mid-parental heterosis (MPH). Our models jointly fitted all the additive, dominance and epistatic effects. The analyses resulted in several important findings: 1) Main components are additive and additive-by-additive effects for GCA and dominance-related effects for SCA and MPH, and additive-by-dominant effect for MPH was partly identified as additive effect; 2) the ranking of factors affecting heterosis was dominance > dominance-by-dominance > over-dominance > complete dominance; and 3) increasing the proportion of F1 hybrids in the population could significantly increase the power to detect dominance-related effects, and slightly reduce the power to detect additive and additive-by-additive effects. Analyses of cotton and rapeseed datasets showed that more additive-by-additive QTL were detected from GCA than from trait phenotype, and fewer QTL were from MPH than from other dependent variables.
Collapse
Affiliation(s)
- Jia Wen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinwang Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guorong Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Dan Xiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Su-Hong Bu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Can Yi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Maryland 20705, USA
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AS, United Kingdom
| | - Jinxing Tu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan-Ming Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
25
|
OsPRR37 and Ghd7 are the major genes for general combining ability of DTH, PH and SPP in rice. Sci Rep 2015; 5:12803. [PMID: 26238949 PMCID: PMC4523830 DOI: 10.1038/srep12803] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 07/06/2015] [Indexed: 11/11/2022] Open
Abstract
Artificial selection of high yield crops and better livestock is paramount importance in breeding programs. Selection of elite parents with preferred traits from a phalanx of inbred lines is extremely laborious, time-consuming and highly random. General combining ability (GCA) was proposed and has been widely used for the evaluation of parents in hybrid breeding for more than half a century. However, the genetic and molecular basis of GCA has been largely overlooked. Here, we present two pleotropic QTLs are accounting for GCA of days to heading (DTH), plant height (PH) and spikelet per panicle (SPP) using an F2-based NCII design, the BC3F2 population as well as a set of nearly isogenic lines (NILs) with five testers. Both GCA1 and GCA2 were loss-of-function gene in low-GCA parent and gain-of-function gene in high-GCA parent, encoding the putative Pseudo-Response Regulators, OsPRR37 and Ghd7, respectively. Overexpression of GCA1 in low-GCA parent significantly increases GCA effects in three traits. Our results demonstrate that two GCA loci associate with OsPRR37 and Ghd7 and reveal that the genes responsible for important agronomic traits could simultaneously account for GCA effects.
Collapse
|
26
|
Jiang L, Ge M, Zhao H, Zhang T. Analysis of heterosis and quantitative trait loci for kernel shape related traits using triple testcross population in maize. PLoS One 2015; 10:e0124779. [PMID: 25919458 PMCID: PMC4412835 DOI: 10.1371/journal.pone.0124779] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 03/03/2015] [Indexed: 11/18/2022] Open
Abstract
Kernel shape related traits (KSRTs) have been shown to have important influences on grain yield. The previous studies that emphasize kernel length (KL) and kernel width (KW) lack a comprehensive evaluation of characters affecting kernel shape. In this study, materials of the basic generations (B73, Mo17, and B73 × Mo17), 82 intermated B73 × Mo17 (IBM) individuals, and the corresponding triple testcross (TTC) populations were used to evaluate heterosis, investigate correlations, and characterize the quantitative trait loci (QTL) for six KSRTs: KL, KW, length to width ratio (LWR), perimeter length (PL), kernel area (KA), and circularity (CS). The results showed that the mid-parent heterosis (MPH) for most of the KSRTs was moderate. The performance of KL, KW, PL, and KA exhibited significant positive correlation with heterozygosity but their Pearson’s R values were low. Among KSRTs, the strongest significant correlation was found between PL and KA with R values was up to 0.964. In addition, KW, PL, KA, and CS were shown to be significant positive correlation with 100-kernel weight (HKW). 28 QTLs were detected for KSRTs in which nine were augmented additive, 13 were augmented dominant, and six were dominance × additive epistatic. The contribution of a single QTL to total phenotypic variation ranged from 2.1% to 32.9%. Furthermore, 19 additive × additive digenic epistatic interactions were detected for all KSRTs with the highest total R2 for KW (78.8%), and nine dominance × dominance digenic epistatic interactions detected for KL, LWR, and CS with the highest total R2 (55.3%). Among significant digenic interactions, most occurred between genomic regions not mapped with main-effect QTLs. These findings display the complexity of the genetic basis for KSRTs and enhance our understanding on heterosis of KSRTs from the quantitative genetic perspective.
Collapse
Affiliation(s)
- Lu Jiang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
| | - Min Ge
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tifu Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail:
| |
Collapse
|
27
|
Bu SH, Xinwang Z, Yi C, Wen J, Jinxing T, Zhang YM. Interacted QTL mapping in partial NCII design provides evidences for breeding by design. PLoS One 2015; 10:e0121034. [PMID: 25822501 PMCID: PMC4379165 DOI: 10.1371/journal.pone.0121034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 02/07/2015] [Indexed: 11/18/2022] Open
Abstract
The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F1 crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F1 hybrids, and all these F1 phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F1 hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study.
Collapse
Affiliation(s)
- Su Hong Bu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhao Xinwang
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Can Yi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jia Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Tu Jinxing
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuan Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement / Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu, China
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
| |
Collapse
|
28
|
Li L, Sun C, Chen Y, Dai Z, Qu Z, Zheng X, Yu S, Mou T, Xu C, Hu Z. QTL mapping for combining ability in different population-based NCII designs: a simulation study. J Genet 2014; 92:529-43. [PMID: 24371174 DOI: 10.1007/s12041-013-0311-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The NCII design (North Carolina mating design II) has been widely applied in studies of combining ability and heterosis. The objective of our research was to estimate how different base populations, sample sizes, testcross numbers and heritability influence QTL analyses of combining ability and heterosis. A series of Monte Carlo simulation experiments with QTL mapping were then conducted for the base population performance, testcross population phenotypic values and the general combining ability (GCA), specific combining ability (SCA) and Hmp (midparental heterosis) datasets. The results indicated that: (i) increasing the number of testers did not necessarily enhance the QTL detection power for GCA, but it was significantly related to the QTL effect. (ii) The QTLs identified in the base population may be different from those from GCA dataset. Similar phenomena can be seen from QTL detected in SCA and Hmp datasets. (iii) The QTL detection power for GCA ranked in the order of DH(RIL) based > F2 based > BC based NCII design, when the heritability was low. The recombinant inbred lines (RILs) (or DHs) allows more recombination and offers higher mapping resolution than other populations. Further, their testcross progeny can be repeatedly generated and phenotyped. Thus, RIL based (or DH based) NCII design was highly recommend for combining ability QTL analysis. Our results expect to facilitate selecting elite parental lines with high combining ability and for geneticists to research the genetic basis of combining ability.
Collapse
Affiliation(s)
- Lanzhi Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Disease and Insect Pests, College of Bio-Safety Science and Technology, Hunan Agricultural University, Changsha, People's Republic of China.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Song G, Guo Z, Liu Z, Qu X, Jiang D, Wang W, Zhu Y, Yang D. The phenotypic predisposition of the parent in F1 hybrid is correlated with transcriptome preference of the positive general combining ability parent. BMC Genomics 2014; 15:297. [PMID: 24755044 PMCID: PMC4023606 DOI: 10.1186/1471-2164-15-297] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/10/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Sprague and Tatum (1942) introduced the concepts of general combining ability (GCA) and specific combining ability (SCA) to evaluate the breeding parents and F1 hybrid performance, respectively. Since then, the GCA was widely used in cross breeding for elite parent selection. However, the molecular basis of GCA remains to unknown. RESULTS We studied the transcriptomes of three varieties and three F1 hybrids using RNA-Sequencing. Transcriptome sequence analysis revealed that the transcriptome profiles of the F1s were similar to the positive GCA-effect parent. Moreover, the expression levels of most differentially expressed genes (DEGs) were equal to the parent with a positive GCA effect. Analysis of the gene expression patterns of gibberellic acid (GA) and flowering time pathways that determine plant height and flowering time in rice validated the preferential transcriptome expression of the parents with positive GCA effect. Furthermore, H3K36me3 modification bias in the Pseudo-Response Regulators (PRR) gene family was observed in the positive GCA effect parents and demonstrated that the phenotype and transcriptome bias in the positive GCA effect parents have been epigenetically regulated by either global modification or specific signaling pathways in rice. CONCLUSIONS The results revealed that the transcriptome profiles and DEGs in the F1s were highly related to phenotype bias to the positive GCA-effect parent. The transcriptome bias toward high GCA parents in F1 hybrids attributed to H3K36me3 modification both on global modification level and specific signaling pathways. Our results indicated the transcriptome profile and epigenetic modification level bias to high GCA parents could be the molecular basis of GCA.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Daichang Yang
- State Key Laboratory of Hybrid Rice and College of Life Sciences, Wuhan University, Luojia Hill, Wuhan 430072, Hubei Province, China.
| |
Collapse
|
30
|
General combining ability of most yield-related traits had a genetic basis different from their corresponding traits per se in a set of maize introgression lines. Genetica 2013; 141:453-61. [PMID: 24135978 DOI: 10.1007/s10709-013-9744-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
Abstract
Evaluation of combining ability is a crucial process in hybrid breeding, and dissection of the genetic basis of combining ability will facilitate hybrid breeding. In this study, molecular markers significantly associated with general combining ability (GCA) of seven yield-related traits and the traits per se were detected in a set of maize introgression lines (ILs) under three environments. Totally 25 and 31 significant loci for GCA and the traits per se were commonly detected under multiple environments, respectively. Correlation analysis and comparison among these significant loci revealed that the genetic basis of GCA of these yield-related traits was generally different from that of the traits per se except for the trait of ear row number. In addition, GCA of the ILs was positively and significantly correlated to the total relative effects of significant GCA loci in the ILs in general, implying that the GCA loci identified in this study would be useful in molecular breeding. Correlation analysis also showed that the GCA of yield per plant was strongly correlated to the GCA of kernel number per row, ear length and 100-kernel-weight, thus these traits were more important in genetic improvement for GCA. Results in this study would provide useful information for hybrid breeding in maize.
Collapse
|