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Liu Q, Wang Y, Fu Y, Du L, Zhang Y, Wang Q, Sun R, Ai N, Feng G, Li C. Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:205. [PMID: 37668671 DOI: 10.1007/s00122-023-04453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
KEY MESSAGE In total, 17 QTLs for lint percentage in short-season cotton, including three stable QTLs, were detected. Twenty-eight differentially expressed genes located within the stable QTLs were identified, and two genes were validated by qRT-PCR. The breeding and use of short-season cotton have significant values in addressing the question of occupying farmlands with either cotton or cereals. However, the fiber yields of short-season cotton varieties are significantly lower than those of middle- and late-maturing varieties. How to effectively improve the fiber yield of short-season cotton has become a focus of cotton research. Here, a high-density genetic map was constructed using genome resequencing and an RIL population generated from the hybridization of two short-season cotton accessions, Dong3 and Dong4. The map contained 4960 bin markers across the 26 cotton chromosomes and spanned 3971.08 cM, with an average distance of 0.80 cM between adjacent markers. Based on the genetic map, quantitative trait locus (QTL) mapping for lint percentage (LP, %), an important yield component trait, was performed. In total, 17 QTLs for LP, including three stable QTLs, qLP-A02, qLP-D04, and qLP-D12, were detected. Three out of 11 non-redundant QTLs overlapped with previously reported QTLs, whereas the other eight were novel QTLs. A total of 28 differentially expressed genes associated with the three stable QTLs were identified using RNA-seq of ovules and fibers at different seed developmental stages from the parental materials. The two genes, Ghir_A02G017640 and Ghir_A02G018500, may be related to LP as determined by further qRT-PCR validation. This study provides useful information for the genetic dissection of LP and promotes the molecular breeding of short-season cotton.
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Affiliation(s)
- Qiao Liu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuanyuan Wang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Yuanzhi Fu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Lei Du
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Yilin Zhang
- Life Science College, Yuncheng University, Yuncheng, 044000, China
| | - Qinglian Wang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Runrun Sun
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Nijiang Ai
- Shihezi Academy of Agricultural Sciences, Shihezi, 832000, China
| | - Guoli Feng
- Shihezi Academy of Agricultural Sciences, Shihezi, 832000, China
| | - Chengqi Li
- Life Science College, Yuncheng University, Yuncheng, 044000, China.
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Niu H, Kuang M, Huang L, Shang H, Yuan Y, Ge Q. Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60. BMC PLANT BIOLOGY 2023; 23:179. [PMID: 37020180 PMCID: PMC10074700 DOI: 10.1186/s12870-023-04147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield. RESULTS Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation. CONCLUSIONS A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Kuang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Longyu Huang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, 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, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, 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, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Yang Y, Qin B, Chen Q, Nie Q, Zhang J, Zhang L, Liu S. Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin. BMC Genomics 2023; 24:13. [PMID: 36627555 PMCID: PMC9830913 DOI: 10.1186/s12864-022-09105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Taraxacum kok-saghyz Rodin (TKS) is a promising commercial alternative natural rubber (NR) yielding plant. Cultivating TKS with a high NR content is an important breeding target, and developing molecular markers related to NR content can effectively accelerate the breeding process of TKS. RESULTS To construct a high-density SNP genetic map and uncover genomic regions related to the NR content in TKS, an F1 mapping population of TKS was constructed by crossing two parents (l66 and X51) with significant differences in NR contents. The NR content of the F1 plants ranged from 0.30 to 15.14% and was distributed normally with a coefficient of variation of 47.61%, indicating quantitative trait inheritance. Then, employing whole-genome resequencing (WGR), a TKS genetic linkage map of 12,680 bin markers comprising 322,439 SNPs was generated. Based on the genetic map and NR content of the F1 population, six quantitative trait loci (QTLs) for NR content with LOD > 4.0 were identified on LG01/Chr01 and LG06/Chr06. Of them, the 2.17 Mb genomic region between qHRC-C6-1 and qHRC-C6-2 on ChrA06, with 65.62% PVE in total, was the major QTL region. In addition, the six QTLs have significant additive genetic effects on NR content and could be used to develop markers for marker-assisted selection (MAS) in TKS with a high NR content. CONCLUSION This work constructed the first high-density TKS genetic map and identified the QTLs and genomic regions controlling the NR content, which provides useful information for fine mapping, map-based cloning, and MAS in TKS.
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Affiliation(s)
- Yushuang Yang
- grid.453499.60000 0000 9835 1415Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, 571101 Haikou, China
| | - Bi Qin
- grid.453499.60000 0000 9835 1415Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, 571101 Haikou, China
| | - Qiuhui Chen
- grid.453499.60000 0000 9835 1415Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, 571101 Haikou, China
| | - Qiuhai Nie
- Beijing Linglong Dandelion Technology and Development Ltd, 101102 Beijing, China
| | - Jichuan Zhang
- grid.48166.3d0000 0000 9931 8406College of Materials and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Liqun Zhang
- grid.48166.3d0000 0000 9931 8406College of Materials and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Shizhong Liu
- grid.453499.60000 0000 9835 1415Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, 571101 Haikou, China
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Dong R, Liu R, Xu Y, Liu W, Sun Y. Effect of foliar and root exposure to polymethyl methacrylate microplastics on biochemistry, ultrastructure, and arsenic accumulation in Brassica campestris L. ENVIRONMENTAL RESEARCH 2022; 215:114402. [PMID: 36167108 DOI: 10.1016/j.envres.2022.114402] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Despite the serious risk of microplastic pollution in the roots and leaves of crops, the phytotoxicity of microplastics (introduced via different exposure routes) in leafy vegetables remain insufficiently understood. Here, the effects of the root and foliar exposure of polymethyl methacrylate microplastic (PMMAMPs) on phytotoxicity, As accumulation, and subcellular distribution were investigated in rapeseed (Brassica campestris L). The relative chlorophyll content under PMMAMPs treatment decreased with time, and the 0.05 g L-1 root exposure decreased it significantly (by 9.97-20.48%, P < 0.05). In addition, superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and ascorbate peroxidase (APX) activities in rapeseed were more sensitive to PMMAMPs introduced through root exposure than through foliar exposure. There was dose-dependent ultrastructural damage, and root exposure had a greater impact than foliar exposure on root tip cells and chloroplasts. PMMAMPs entered the shoots and roots of rapeseed through root exposure. Under foliar exposure, PMMAMPs promoted As accumulation in rapeseed by up to 75.6% in shoots and 68.2% in roots compared to that under control (CK). As content in cell wall under PMMAMP treatments was 3.6-5.3 times higher than that of CK, as indicated by subcellular component results. In general, root exposure to PMMAMPs resulted in a stronger physiological impact and foliar exposure led to increased As accumulation in rapeseed.
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Affiliation(s)
- Ruyin Dong
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin, 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin, 300191, China
| | - Rongle Liu
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin, 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin, 300191, China.
| | - Yingming Xu
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin, 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin, 300191, China
| | - Weitao Liu
- College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Yuebing Sun
- Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, Ministry of Agriculture and Rural Affairs (MARA), Agro-Environmental Protection Institute, MARA, Tianjin, 300191, China; Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Agro-Environmental Protection Institute, MARA, Tianjin, 300191, China.
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