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Li Z, Jia Z, Li J, Kang D, Li M, Ma S, Cheng Q, Shen H, Sun L. Development of a 45K pepper GBTS liquid-phase gene chip and its application in genome-wide association studies. FRONTIERS IN PLANT SCIENCE 2024; 15:1405190. [PMID: 38984163 PMCID: PMC11231373 DOI: 10.3389/fpls.2024.1405190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/13/2024] [Indexed: 07/11/2024]
Abstract
Introduction Pepper (Capsicum spp.) is a vegetable that is cultivated globally and has undergone extensive domestication, leading to a significant diversification in its agronomic traits. With the advancement of genomics in pepper and the reduction in sequencing costs, the high-throughput detection of single nucleotide polymorphisms (SNPs) and small insertions-deletions (indels) has become increasingly critical for analyzing pepper germplasms and improving breeding programs. As a result, there is a pressing need for a cost-effective, high-throughput, and versatile technique suitable for both foreground and background selection in pepper breeding. Methods In the present study, Python-based web scraping scripts were utilized to systematically extract data from published literatures and relevant sequence databases focusing on pepper genomes. Subsequent to data extraction, SNPs and indels were meticulously identified and filtered. This process culminated in the delineation of core polymorphic sites, which were instrumental in the development of specific probes. Following this, comprehensive phenotypic and genotypic analyses were conducted on a diverse collection of 420 pepper germplasms. Concurrently, a genome-wide association study (GWAS) was conducted to elucidate the genetic determinants of helical fruit shape in peppers. Results In this study, a 45K pepper Genotyping-By-Target-Sequencing (GBTS) liquid-phase gene chip was developed on the GenoBaits platform. This chip is composed of 45,389 probes, of which 42,535 are derived from core polymorphic sites (CPS) in the background genetic landscape, while 2,854 are associated with foreground agronomic traits, spanning across 43 traits. The CPS probes are spaced at an average interval of 68 Kb. We have assessed the performance of this chip on 420 pepper germplasms, with successful capture of target DNA fragments by 45,387 probes. Furthermore, the probe capture ratio surpassed 70% in 410 of the 420 germplasms tested. Using this chip, we have efficiently genotyped 273 germplasms for spiciness levels and elucidated the genetic relationships among 410 pepper germplasms. Our results allowed for precise clustering of sister lines and C. chinense germplasms. In addition, through a GWAS for helical fruit shape, we identified three quantitative trait loci (QTLs): heli2.1, heli11.1, and heli11.2. Within the heli11.1 QTL, a gene encoding the tubulin alpha chain was identified, suggesting its potential role in the helical growth pattern of pepper fruits. Discussion In summary, the 45K pepper GBTS liquid-phase gene chip offers robust detection of polymorphic sites and is a promising tool for advancing research into pepper germplasm and the breeding of new pepper varieties.
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Affiliation(s)
- Zixiong Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Zhiqi Jia
- Department of Vegetable Science, College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Jisuo Li
- Beijing Bona Oriental Agricultural Technology Development Co., Ltd, Beijing, China
| | - Dongmu Kang
- Beijing Bona Oriental Agricultural Technology Development Co., Ltd, Beijing, China
| | - Mingxuan Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Shijie Ma
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Qing Cheng
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
| | - Liang Sun
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing, China
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Wang J, Wang E, Cheng S, Ma A. Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA. FRONTIERS IN PLANT SCIENCE 2024; 15:1361621. [PMID: 38504905 PMCID: PMC10948542 DOI: 10.3389/fpls.2024.1361621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 01/30/2024] [Indexed: 03/21/2024]
Abstract
Grain number per spike, a pivotal agronomic trait dictating wheat yield, lacks a comprehensive understanding of its underlying mechanism in Pubing3228, despite the identification of certain pertinent genes. Thus, our investigation sought to ascertain molecular markers and candidate regions associated with grain number per spike through a high-density genetic mapping approach that amalgamates site-specific amplified fragment sequencing (SLAF-seq) and bulked segregation analysis (BSA). To facilitate this, we conducted a comparative analysis of two wheat germplasms, Pubing3228 and Jing4839, known to exhibit marked discrepancies in spike shape. By leveraging this methodology, we successfully procured 2,810,474 SLAF tags, subsequently resulting in the identification of 187,489 single nucleotide polymorphisms (SNPs) between the parental strains. We subsequently employed the SNP-index association algorithm alongside the extended distribution (ED) association algorithm to detect regions associated with the trait. The former algorithm identified 24 trait-associated regions, whereas the latter yielded 70. Remarkably, the intersection of these two algorithms led to the identification of 25 trait-associated regions. Amongst these regions, we identified 399 annotated genes, including three genes harboring non-synonymous mutant SNP loci. Notably, the APETALA2 (AP2) transcription factor families, which exhibited a strong correlation with spike type, were also annotated. Given these findings, it is plausible to hypothesize that these genes play a critical role in determining spike shape. In summation, our study contributes significant insights into the genetic foundation of grain number per spike. The molecular markers and candidate regions we have identified can be readily employed for marker-assisted breeding endeavors, ultimately leading to the development of novel wheat cultivars possessing enhanced yield potential. Furthermore, conducting further functional analyses on the identified genes will undoubtedly facilitate a comprehensive elucidation of the underlying mechanisms governing spike development in wheat.
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Affiliation(s)
- Jiansheng Wang
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, Henan, China
- Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan, Henan, China
| | - Erwei Wang
- Pingdingshan Academy of Agricultural Science, Pingdingshan, Henan, China
| | - Shiping Cheng
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, Henan, China
- Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan, Henan, China
| | - Aichu Ma
- Pingdingshan Academy of Agricultural Science, Pingdingshan, Henan, China
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Zhang S, Wang H, Li X, Tang L, Cai X, Liu C, Zhang X, Zhang J. Aspartyl proteases identified as candidate genes of a fiber length QTL, qFL D05, that regulates fiber length in cotton (Gossypium hirsutum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:59. [PMID: 38407588 DOI: 10.1007/s00122-024-04559-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/20/2024] [Indexed: 02/27/2024]
Abstract
KEY MESSAGE GhAP genes were identified as the candidates involved in cotton fiber length under the scope of fine mapping a stable fiber length QTL, qFLD05. Moreover, the transcription factor GhWRKY40 positively regulated GhAP3 to decrease fiber length. Fiber length (FL) is an economically important fiber quality trait. Although several genes controlling cotton fiber development have been identified, our understanding of this process remains limited. In this study, an FL QTL (qFLD05) was fine-mapped to a 216.9-kb interval using a secondary F2:3 population derived from the upland hybrid cultivar Ji1518. This mapped genomic segment included 15 coding genes, four of which were annotated as aspartyl proteases (GhAP1-GhAP4). GhAPs were identified as candidates for qFLD05 as the sequence variations in GhAPs were associated with FL deviations in the mapping population, and functional validation of GhAP3 and GhAP4 indicated a longer FL following decreases in their expression levels through virus-induced gene silencing (VIGS). Subsequently, the potential involvement of GhWRKY40 in the regulatory network was revealed: GhWRKY40 positively regulated GhAP3's expression according to transcriptional profiling, VIGS, yeast one-hybrid assays and dual-luciferase experiments. Furthermore, alterations in the expression of the eight previously reported cotton FL-responsive genes from the above three VIGS lines (GhAP3, GhAP4 and GhWRKY40) implied that MYB5_A12 was involved in the GhWRKY40-GhAP network. In short, we unveiled the unprecedented FL regulation roles of GhAPs in cotton, which was possibly further regulated by GhWRKY40. These findings will reveal the genetic basis of FL development associated with qFLD05 and be beneficial for the marker-assisted selection of long-staple cotton.
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Affiliation(s)
- Sujun Zhang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Haitao Wang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Xinghe Li
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Liyuan Tang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Xiao Cai
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Cunjing Liu
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Xiangyun Zhang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agricultural and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang, 050051, Hebei, China.
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Zhong J, Cui J, Miao M, Hu F, Dong J, Liu J, Zhong C, Cheng J, Hu K. A point mutation in MC06g1112 encoding FLOWERING LOCUS T decreases the first flower node in bitter gourd ( Momordica charantia L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1153208. [PMID: 37881613 PMCID: PMC10595031 DOI: 10.3389/fpls.2023.1153208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023]
Abstract
In Cucurbitaceae crops, the first flower node (FFN) is an important agronomic trait which can impact the onset of maturity, the production of female flowers, and yield. However, the gene responsible for regulating FFN in bitter gourd is unknown. Here, we used a gynoecious line (S156G) with low FFN as the female parent and a monoecious line (K8-201) with high FFN as the male parent to obtain F1 and F2 generations. Genetic analysis indicated that the low FFN trait was incompletely dominant over the high FFN trait. A major quantitative trait locus (QTL)-Mcffn and four minor effect QTLs-Mcffn1.1, Mcffn1.2, Mcffn1.3, and Mcffn1.4 were detected by whole-genome re-sequencing-based QTL mapping in the S156G×K8-201 F2 population (n=234) cultivated in autumn 2019. The Mcffn locus was further supported by molecular marker-based QTL mapping in three S156G×K8-201 F2 populations planted in autumn 2019 (n=234), autumn 2020 (n=192), and spring 2022 (n=205). Then, the Mcffn locus was fine-mapped into a 77.98-kb physical region on pseudochromosome MC06 using a large S156G×K8-201 F2 population (n=2,402). MC06g1112, which is a homolog of FLOWERING LOCUS T (FT), was considered as the most likely Mcffn candidate gene according to both expression and sequence variation analyses between parental lines. A point mutation (C277T) in MC06g1112, which results in a P93S amino acid mutation between parental lines, may be responsible for decreasing FFN in bitter gourd. Our findings provide a helpful resource for the molecular marker-assisted selective breeding of bitter gourd.
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Affiliation(s)
- Jian Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Junjie Cui
- Department of Horticulture, Foshan University, Foshan, China
| | - Mingjun Miao
- Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Fang Hu
- Henry Fok School of Biology and Agricultural, Shaoguan University, Shaoguan, China
| | - Jichi Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Chunfeng Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiaowen Cheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Kailin Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, South China Agricultural University, Guangzhou, China
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Wu Y, Shi H, Yu H, Ma Y, Hu H, Han Z, Zhang Y, Zhen Z, Yi L, Hou J. Combined GWAS and Transcriptome Analyses Provide New Insights Into the Response Mechanisms of Sunflower Against Drought Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:847435. [PMID: 35592557 PMCID: PMC9111542 DOI: 10.3389/fpls.2022.847435] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/31/2022] [Indexed: 05/25/2023]
Abstract
Sunflower is one of the most important oil crops in the world, and drought stress can severely limit its production and quality. To understand the underlying mechanism of drought tolerance, and identify candidate genes for drought tolerance breeding, we conducted a combined genome-wide association studies (GWAS) and RNA-seq analysis. A total of 226 sunflower inbred lines were collected from different regions of China and other countries. Eight phenotypic traits were evaluated under control and drought stress conditions. Genotyping was performed using a Specific-Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 934.08 M paired-end reads were generated, with an average Q30 of 91.97%. Based on the 243,291 polymorphic SLAF tags, a total of 94,162 high-quality SNPs were identified. Subsequent analysis of linkage disequilibrium (LD) and population structure in the 226 accessions was carried out based on the 94,162 high-quality SNPs. The average LD decay across the genome was 20 kb. Admixture analysis indicated that the entire population most likely originated from 11 ancestors. GWAS was performed using three methods (MLM, FarmCPU, and BLINK) simultaneously. A total of 80 SNPs showed significant associations with the 8 traits (p < 1.062 × 10-6). Next, a total of 118 candidate genes were found. To obtain more reliable candidate genes, RNA-seq analysis was subsequently performed. An inbred line with the highest drought tolerance was selected according to phenotypic traits. RNA was extracted from leaves at 0, 7, and 14 days of drought treatment. A total of 18,922 differentially expressed genes were obtained. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed up-regulated genes were mainly enriched in the branched-chain amino acid catabolic process, while the down-regulated genes were mainly enriched in the photosynthesis-related process. Six DEGs were randomly selected from all DEGs for validation; these genes showed similar patterns in RNA-seq and RT-qPCR analysis, with a correlation coefficient of 0.8167. Through the integration of the genome-wide association study and the RNA-sequencing, 14 candidate genes were identified. Four of them (LOC110885273, LOC110872899, LOC110891369, LOC110920644) were abscisic acid related protein kinases and transcription factors. These genes may play an important role in sunflower drought response and will be used for further study. Our findings provide new insights into the response mechanisms of sunflowers against drought stress and contribute to further genetic breeding.
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Affiliation(s)
- Yang Wu
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Huimin Shi
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Haifeng Yu
- Institute of Crop Breeding and Cultivation, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, China
| | - Yu Ma
- Institute of Crop Breeding and Cultivation, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, China
| | - Haibo Hu
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhigang Han
- Institute of Crop Breeding and Cultivation, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, China
| | - Yonghu Zhang
- Institute of Crop Breeding and Cultivation, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, China
| | - Zilong Zhen
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Liuxi Yi
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
| | - Jianhua Hou
- College of Agricultural, Inner Mongolia Agricultural University, Hohhot, China
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Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
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Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Sun C, Liu Y, Li Q, Wang B, Chen S, Deng J, Ma D, Yang Y. Rapid Identification of a Stripe Rust Resistance Gene YrXK in Chinese Wheat Line Xike01015 Using Specific Locus Amplified Fragment (SLAF) Sequencing. PLANT DISEASE 2022; 106:282-288. [PMID: 34253044 DOI: 10.1094/pdis-12-20-2648-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Wheat stripe rust, an airborne fungal disease caused by Puccinia striiformis Westend. f. sp. tritici, is one of the most devastating diseases of wheat. Chinese wheat cultivar Xike01015 displays high levels of all-stage resistance (ASR) to the current predominant P. striiformis f. sp. tritici race CYR33. In this study, a single dominant gene, designated YrXk, was identified in Xike01015 conferring resistance to CYR33 with genetic analysis of F2 and BC1 populations from a cross of Mingxian169 (susceptible) and Xike01015. The specific length amplified fragment sequencing (SLAF-seq) strategy was used to construct a linkage map in the F2 population. Quantitative trait loci (QTL) analysis mapped YrXk to a 12.4-Mb segment on chromosome1 BS, explaining >86.96% of the phenotypic variance. Gene annotation in the QTL region identified three differential expressed candidate genes, TraesCS1B02G168600.1, TraesCS1B02G170200.1, and TraesCS1B02G172400.1. The qRT-PCR results showed that TraesCS1B02G172400.1 and TraesCS1B02G168600.1 are upregulated and that TraesCS1B02G170200.1 is slightly downregulated after inoculation with CYR33 in the seedling stage, which indicates that these genes may function in wheat resistance to stripe rust. The results of this study can be used in wheat breeding for improving resistance to stripe rust.
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Affiliation(s)
- Cai Sun
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, P.R. China
- College of Plant Protection, Southwest University, Beibei 400700, P.R. China
| | - Yike Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430064, Hubei, P.R. China
| | - Qiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling 712100, Shaanxi, P.R. China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling 712100, Shaanxi, P.R. China
| | - Shuhui Chen
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, P.R. China
| | - Jianxin Deng
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, P.R. China
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430064, Hubei, P.R. China
| | - Dongfang Ma
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, P.R. China
- Institute of Food Crops, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Wuhan 430064, Hubei, P.R. China
| | - Yuheng Yang
- College of Plant Protection, Southwest University, Beibei 400700, P.R. China
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Li J, Yu X, Zhang S, Yu Z, Li J, Jin X, Zhang X, Yang D. Identification of starch candidate genes using SLAF-seq and BSA strategies and development of related SNP-CAPS markers in tetraploid potato. PLoS One 2021; 16:e0261403. [PMID: 34932571 PMCID: PMC8691606 DOI: 10.1371/journal.pone.0261403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
Potato starch is an essential nutrient for humans and is widely used worldwide. Locating relevant genomic regions, mining stable genes and developing candidate gene markers can promote the breeding of new high-starch potato varieties. A total of 106 F1 individuals and their parents (YSP-4 × MIN-021) were used as test materials, from which 20 plants with high starch content and 20 with low starch content were selected to construct DNA pools for site-specific amplified fragment sequencing (SLAF-seq) and bulked segregation analysis (BSA). A genomic region related to the starch traits was first identified in the 0–5.62 Mb of chromosome 2 in tetraploid potato. In this section, a total of 41 non-synonymous genes, which were considered as candidate genes related to the starch trait, were annotated through a basic local alignment search tool (BLAST) search of multiple databases. Six candidate genes for starch (PGSC0003DMG400017793, PGSC0003DMG400035245, PGSC0003DMG400036713, PGSC0003DMG400040452, PGSC0003DMG400006636 and PGSC0003DMG400044547) were further explored. In addition, cleaved amplified polymorphic sequence (CAPS) markers were developed based on single nucleotide polymorphism (SNP) sites associated with the starch candidate genes. SNP-CAPS markers chr2-CAPS6 and chr2-CAPS21 were successfully developed and validated with the F2 population and 24 tetraploid potato varieties (lines). Functional analysis and cloning of the candidate genes associated with potato starch will be performed in further research, and the SNP-CAPS markers chr2-CAPS6 and chr2-CAPS21 can be further used in marker-assisted selection breeding of tetraploid potato varieties with high starch content.
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Affiliation(s)
- Jiaqi Li
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaoxia Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Sheng Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- * E-mail: (SZ); (ZY)
| | - Zhuo Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- * E-mail: (SZ); (ZY)
| | - Jingwei Li
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xinghong Jin
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xia Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Dongsheng Yang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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Yuan X, Fang R, Zhou K, Huang Y, Lei G, Wang X, Chen X. The APETALA2 homolog CaFFN regulates flowering time in pepper. HORTICULTURE RESEARCH 2021; 8:208. [PMID: 34719686 PMCID: PMC8558333 DOI: 10.1038/s41438-021-00643-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 06/13/2023]
Abstract
Flowering time is an important agronomic trait that contributes to fitness in plants. However, the genetic basis of flowering time has not been extensively studied in pepper. To understand the genetics underlying flowering time, we constructed an F2 population by crossing a spontaneous early flowering mutant and a late-flowering pepper line. Using bulked segregant RNA-seq, a major locus controlling flowering time in this population was mapped to the end of chromosome 2. An APETALA2 (AP2) homolog (CaFFN) cosegregated with flowering time in 297 individuals of the F2 population. A comparison between the parents revealed a naturally occurring rare SNP (SNP2T > C) that resulted in the loss of a start codon in CaFFN in the early flowering mutant. Transgenic Nicotiana benthamiana plants with high CaFFN expression exhibited a delay in flowering time and floral patterning defects. On the other hand, pepper plants with CaFFN silencing flowered early. Therefore, the CaFFN gene acts as a flowering repressor in pepper. CaFFN may function as a transcriptional activator to activate the expression of CaAGL15 and miR156e and as a transcriptional repressor to repress the expression of CaAG, CaAP1, CaSEP3, CaSOC1, and miR172b based on a qRT-PCR assay. Direct activation of CaAGL15 by CaFFN was detected using yeast one-hybrid and dual-luciferase reporter assays, consistent with the hypothesis that CaFFN regulates flowering time. Moreover, the CaFFN gene association analysis revealed a significant association with flowering time in a natural pepper population, indicating that the CaFFN gene has a broad effect on flowering time in pepper. Finally, the phylogeny, evolutionary expansion and expression patterns of CaFFN/AP2 homologs were analyzed to provide valuable insight into CaFFN. This study increases our understanding of the involvement of CaFFN in controlling flowering time in pepper, thus making CaFFN a target gene for breeding early maturing pepper.
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Affiliation(s)
- Xinjie Yuan
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Rong Fang
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Kunhua Zhou
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Yueqin Huang
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Gang Lei
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Xuejun Chen
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, 330200, Nanchang, China.
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Zhan H, Wang Y, Zhang D, Du C, Zhang X, Liu X, Wang G, Zhang S. RNA-seq bulked segregant analysis combined with KASP genotyping rapidly identified PmCH7087 as responsible for powdery mildew resistance in wheat. THE PLANT GENOME 2021; 14:e20120. [PMID: 34309200 DOI: 10.1002/tpg2.20120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Powdery mildew causes considerable yield losses in common wheat (Triticum aestivum L.) production. Mapping and cloning powdery mildew-resistant quantitative trait loci can benefit stable yield production by facilitating the breeding of resistant varieties. In this study, we used the powdery mildew resistance introgression line 'CH7087' (harboring the resistance gene PmCH7087) and developed a large F2 population and a corresponding F2:3 segregation population containing 2,000 family lines for molecular mapping of PmCH7087. Genetic analysis demonstrated that the resistance phenotype was controlled by a single dominant gene. According to the performance exhibited by the F2:3 lines, 50 resistant lines and 50 susceptible lines without phenotype segregation were chosen for pooling and bulked segregant RNA sequencing (BSR-Seq) analysis. A region spanning 42.77 Mb was identified, and genotyping of an additional 183 F2:3 lines with extreme phenotypes using 20 kompetitive allele-specific polymerase chain reaction (KASP) markers in the BSR-Seq mapping regions confirmed this region and narrowed it to 9.68 Mb, in which 45 genes were identified and annotated. Five of these transcripts harbored nonsynonymous single nucleotide polymorphisms between the two parents, with the transcripts of TraesCS2B01G302800 being involved in signal transduction. Furthermore, TraesCS2B01G302800.2 was annotated as the closest homologue of serine/threonine-protein kinase PBS1, a typical participant in the plant disease immune response, indicating that TraesCS2B01G302800 was the candidate gene of PmCH7087. Our results may facilitate future research attempting to improve powdery mildew resistance in wheat and to identify candidate genes for further verification and gene cloning.
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Affiliation(s)
- Haixian Zhan
- Institute of Pharmaceutical & Food Engineering, Shanxi Univ. of Chinese Medicine, Jingzhong, 030619, China
| | - Yingli Wang
- Institute of Pharmaceutical & Food Engineering, Shanxi Univ. of Chinese Medicine, Jingzhong, 030619, China
| | - Dan Zhang
- Institute of Pharmaceutical & Food Engineering, Shanxi Univ. of Chinese Medicine, Jingzhong, 030619, China
| | - Chenhui Du
- Institute of Pharmaceutical & Food Engineering, Shanxi Univ. of Chinese Medicine, Jingzhong, 030619, China
| | - Xiaojun Zhang
- College of Agriculture, Shanxi Agricultural Univ., Taiyuan, 030032, China
| | - Xiaoli Liu
- Institute of Pharmaceutical & Food Engineering, Shanxi Univ. of Chinese Medicine, Jingzhong, 030619, China
| | - Guangyuan Wang
- College of Agriculture, Shanxi Agricultural Univ., Taiyuan, 030032, China
| | - Shuosheng Zhang
- Institute of Pharmaceutical & Food Engineering, Shanxi Univ. of Chinese Medicine, Jingzhong, 030619, China
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11
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Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
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Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
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Genetic Improvement of Cereals and Grain Legumes. Genes (Basel) 2020; 11:genes11111255. [PMID: 33113769 PMCID: PMC7692374 DOI: 10.3390/genes11111255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
The anticipated population growth by 2050 will be coupled with increased food demand. To achieve higher and sustainable food supplies in order to feed the global population by 2050, a 2.4% rise in the yield of major crops is required. The key to yield improvement is a better understanding of the genetic variation and identification of molecular markers, quantitative trait loci, genes, and pathways related to higher yields and increased tolerance to biotic and abiotic stresses. Advances in genetic technologies are enabling plant breeders and geneticists to breed crop plants with improved agronomic traits. This Special Issue is an effort to report the genetic improvements by adapting genomic techniques and genomic selection.
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13
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Okuda Y, Ito M, Shimada Y, Ishigami M, Matsumoto T. Morphological, cytological and genetic analyzes of the 'sango' mutant with the defects in basidiocarp development in edible mushroom Pleurotus pulmonarius. FEMS Microbiol Lett 2020; 366:5626343. [PMID: 31730201 DOI: 10.1093/femsle/fnz227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/08/2019] [Indexed: 11/15/2022] Open
Abstract
A spontaneous, morphological variation 'sango' was observed in the progeny of a Pleurotus pulmonarius (Fr.) Quél. wild-type basidiocarp (also known as fruiting body) collected from the field. This variant developed wart- and coral-like structures instead of normal basidiocarps. Microscopic analysis showed that the sango phenotype had defects in the differentiation of the pileus and hymenium. Basidiocarp phenotypic data analysis in the progenies revealed that the sango trait is a heritable mutation character controlled by a single recessive gene. This mutation locus was mapped on linkage group III of a previously constructed genetic linkage map by amplified fragment length polymorphism (AFLP) technique in P. pulmonarius. Four AFLP markers identified by bulked segregant analysis showed linkage to the sango mutation locus, with the genetic distance ranging from 0 to 2.1 cM. Of these markers, one marker was co-segregated with the sango mutation locus. This knowledge will be a useful foundation for practical breeding as well as for elucidating molecular mechanisms in basidiocarp development of main edible mushrooms.
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Affiliation(s)
- Yasuhito Okuda
- Contribution No. 418 from the Tottori Mycological Institute, 211 Kokoge, Tottori 689-1125, Japan
| | - Mikinari Ito
- Faculty of Agriculture, Tottori University, 4-101 Koyamacho-Minami, Tottori 680-8553, Japan
| | - Yu Shimada
- Faculty of Agriculture, Tottori University, 4-101 Koyamacho-Minami, Tottori 680-8553, Japan
| | - Masato Ishigami
- Faculty of Agriculture, Tottori University, 4-101 Koyamacho-Minami, Tottori 680-8553, Japan
| | - Teruyuki Matsumoto
- Faculty of Agriculture, Tottori University, 4-101 Koyamacho-Minami, Tottori 680-8553, Japan
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Hao N, Han D, Huang K, Du Y, Yang J, Zhang J, Wen C, Wu T. Genome-based breeding approaches in major vegetable crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1739-1752. [PMID: 31728564 DOI: 10.1007/s00122-019-03477-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/09/2019] [Indexed: 05/09/2023]
Abstract
Vegetable crops are major nutrient sources for humanity and have been well-cultivated since thousands of years of domestication. With the rapid development of next-generation sequencing and high-throughput genotyping technologies, the reference genome of more than 20 vegetables have been well-assembled and published. Resequencing approaches on large-scale germplasm resources have clarified the domestication and improvement of vegetable crops by human selection; its application on genetic mapping and quantitative trait locus analysis has led to the discovery of key genes and molecular markers linked to important traits in vegetables. Moreover, genome-based breeding has been utilized in many vegetable crops, including Solanaceae, Cucurbitaceae, Cruciferae, and other families, thereby promoting molecular breeding at a single-nucleotide level. Thus, genome-wide SNP markers have been widely used, and high-throughput genotyping techniques have become one of the most essential methods in vegetable breeding. With the popularization of gene editing technology research on vegetable crops, breeding efficiency can be rapidly increased, especially by combining the genomic and variomic information of vegetable crops. This review outlines the present genome-based breeding approaches used for major vegetable crops to provide insights into next-generation molecular breeding for the increasing global population.
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Affiliation(s)
- Ning Hao
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China
| | - Deguo Han
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China
| | - Ke Huang
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Yalin Du
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
| | - Tao Wu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China.
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China.
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15
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Zhang S, Li B, Chen Y, Shaibu AS, Zheng H, Sun J. Molecular-Assisted Distinctness and Uniformity Testing Using SLAF-Sequencing Approach in Soybean. Genes (Basel) 2020; 11:E175. [PMID: 32041312 PMCID: PMC7074437 DOI: 10.3390/genes11020175] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/27/2022] Open
Abstract
Distinctness, uniformity and stability (DUS) testing of cultivars through morphological descriptors is an important and compulsory part of soybean breeding. Molecular markers are usually more effective and accurate in describing the genetic features for the identification and purity assessment of cultivars. In the present study, we assessed the distinctness and uniformity of five soybean cultivars using both single nucleotide polymorphism (SNP) markers developed by specific-locus amplified fragment sequencing (SLAF-seq) technology, and simple sequence repeat (SSR) markers. The phylogenetic tree and principal component analysis (PCA) from both the SLAF-seq and SSR methods showed a clear distinction among cultivars Zhonghuang 18, Zhonghuang 68 and Zhonghuang 35, while no clear distinction was observed between cultivars Zhonghuang 13 and Hedou 13. Using the SLAF-seq method, we determined the proportion of homozygous loci for the five soybean cultivars. The heterozygosity of each individual plant was estimated for the assessment of cultivar purity and the purity levels of the five soybean cultivars ranged from 91.89% to 93.96%. To further validate the applicability of the SLAF-seq approach for distinctness testing, we used the SNP information of 150 soybean cultivars with different origins. The cultivars were also distinguished clearly. Taken together, SLAF-seq can be used as an accurate and reliable method in the assessment of the distinctness and uniformity of soybean cultivars.
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Affiliation(s)
- Shengrui Zhang
- The National Engineering Laboratory for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.Z.); (B.L.); (Y.C.); (A.S.S.)
| | - Bin Li
- The National Engineering Laboratory for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.Z.); (B.L.); (Y.C.); (A.S.S.)
| | - Ying Chen
- The National Engineering Laboratory for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.Z.); (B.L.); (Y.C.); (A.S.S.)
| | - Abdulwahab S. Shaibu
- The National Engineering Laboratory for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.Z.); (B.L.); (Y.C.); (A.S.S.)
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China;
| | - Junming Sun
- The National Engineering Laboratory for Crop Molecular Breeding, MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, China; (S.Z.); (B.L.); (Y.C.); (A.S.S.)
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16
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Du H, Wen C, Zhang X, Xu X, Yang J, Chen B, Geng S. Identification of a Major QTL ( qRRs-10.1) That Confers Resistance to Ralstonia solanacearum in Pepper ( Capsicum annuum) Using SLAF-BSA and QTL Mapping. Int J Mol Sci 2019; 20:ijms20235887. [PMID: 31771239 PMCID: PMC6928630 DOI: 10.3390/ijms20235887] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/04/2019] [Accepted: 11/21/2019] [Indexed: 11/24/2022] Open
Abstract
The soilborne pathogen Ralstonia solanacearum is the causal agent of bacterial wilt (BW), a major disease of pepper (Capsicum annuum). The genetic basis of resistance to this disease in pepper is not well known. This study aimed to identify BW resistance markers in pepper. Analysis of the dynamics of bioluminescent R. solanacearum colonization in reciprocal grafts of a resistant (BVRC 1) line and a susceptible (BVRC 25) line revealed that the resistant rootstock effectively suppressed the spreading of bacteria into the scion. The two clear-cut phenotypic distributions of the disease severity index in 440 F2 plants derived from BVRC 25 × BVRC 1 indicated that a major genetic factor as well as a few minor factors that control BW resistance. By specific-locus amplified fragment sequencing combined with bulked segregant analysis, two adjacent resistance-associated regions on chromosome 10 were identified. Quantitative trait (QTL) mapping revealed that these two regions belong to a single QTL, qRRs-10.1. The marker ID10-194305124, which reached a maximum log-likelihood value at 9.79 and accounted for 19.01% of the phenotypic variation, was located the closest to the QTL peak. A cluster of five predicted R genes and three defense-related genes, which are located in close proximity to the significant markers ID10-194305124 or ID10-196208712, are important candidate genes that may confer BW resistance in pepper.
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17
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Huang L, Tang W, Bu S, Wu W. BRM: a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing. Bioinformatics 2019; 36:2150-2156. [DOI: 10.1093/bioinformatics/btz861] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/02/2019] [Accepted: 11/17/2019] [Indexed: 12/13/2022] Open
Abstract
Abstract
Motivation
Bulked segregant analysis by deep sequencing (BSA-seq) has been widely used for quantitative trait locus (QTL) mapping in recent years. A number of different statistical methods for BSA-seq have been proposed. However, determination of significance threshold, the key point for QTL identification, remains to be a problem that has not been well solved due to the difficulty of multiple testing correction. In addition, estimation of the confidence interval is also a problem to be solved.
Results
In this paper, we propose a new statistical method for BSA-seq, named Block Regression Mapping (BRM). BRM is robust to sequencing noise and is applicable to the case of low sequencing depth. Significance threshold can be reasonably determined by taking multiple testing correction into account. Meanwhile, the confidence interval of QTL position can also be estimated.
Availability and implementation
The R scripts of our method are open source under GPLv3 license at https://github.com/huanglikun/BRM.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Likun Huang
- Fujian Key Laboratory of Crop Breeding by Design, Fuzhou, Fujian 350002
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Weiqi Tang
- Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou, Fujian 350108, China
| | - Suhong Bu
- Fujian Key Laboratory of Crop Breeding by Design, Fuzhou, Fujian 350002
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
| | - Weiren Wu
- Fujian Key Laboratory of Crop Breeding by Design, Fuzhou, Fujian 350002
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002
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18
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Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper ( Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS. Int J Mol Sci 2019; 20:ijms20225675. [PMID: 31766117 PMCID: PMC6888518 DOI: 10.3390/ijms20225675] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022] Open
Abstract
There are many agronomic traits of pepper (Capsicum L.) with abundant phenotypes that can benefit pepper growth. Using specific-locus amplified fragment sequencing (SLAF-seq), a genome-wide association study (GWAS) of 36 agronomic traits was carried out for 287 representative pepper accessions. To ensure the accuracy and reliability of the GWAS results, we analyzed the genetic diversity, distribution of labels (SLAF tags and single nucleotide polymorphisms (SNPs)) and population differentiation and determined the optimal statistical model. In our study, 1487 SNPs were highly significantly associated with 26 agronomic traits, and 2126 candidate genes were detected in the 100-kb region up- and down-stream near these SNPs. Furthermore, 13 major association peaks were identified for 11 key agronomic traits. Then we examined the correlations among the 36 agronomic traits and analyzed SNP distribution and found 37 SNP polymerization regions (total size: 264.69 Mbp) that could be selected areas in pepper breeding. We found that the stronger the correlation between the two traits, the greater the possibility of them being in more than one polymerization region, suggesting that they may be linked or that one pleiotropic gene controls them. These results provide a theoretical foundation for future multi-trait pyramid breeding of pepper. Finally, we found that the GWAS signals were highly consistent with those from the nuclear restorer-of-fertility (Rf) gene for cytoplasmic male sterility (CMS), verifying their reliability. We further identified Capana06g002967 and Capana06g002969 as Rf candidate genes by functional annotation and expression analysis, which provided a reference for the study of cytoplasmic male sterility in Capsicum.
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Zhang XF, Wang GY, Dong TT, Chen B, Du HS, Li CB, Zhang FL, Zhang HY, Xu Y, Wang Q, Geng SS. High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.). BMC PLANT BIOLOGY 2019; 19:167. [PMID: 31035914 PMCID: PMC6489210 DOI: 10.1186/s12870-019-1753-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/31/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.). The trait is controlled by quantitative trait loci (QTL); however, studies have been limited on QTL mapping and genes contributing to the trait. RESULTS In this study, we developed a high density genetic map using specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput strategy for de novo single nucleotide polymorphism discovery, based on 146 recombinant inbred lines (RILs) derived from an intraspecific cross between PM702 and FS871. The map contained 9328 SLAF markers on 12 linkage groups (LGs), and spanned a total genetic distance of 2009.69 centimorgan (cM) with an average distance of 0.22 cM. The sequencing depth for the map was 72.39-fold in the male parent, 57.04-fold in the female parent, and 15.65-fold in offspring. Using the genetic map, two major QTLs, named Ffn2.1 and Ffn2.2, identified on LG02 were strongly associated with FFN, with a phenotypic variance explanation of 28.62 and 19.56%, respectively. On the basis of the current annotation of C. annuum cv. Criollo de Morelos (CM334), 59 candidate genes were found within the Ffn2.1 and Ffn2.2 region, but only 3 of 59 genes were differentially expressed according to the RNA-seq results. Eventually we identified one gene associated with the FFN based on the function through GO, KEGG, and Swiss-prot analysis. CONCLUSIONS Our research showed that the construction of high-density genetic map using SLAF-seq is a valuable tool for fine QTL mapping. The map we constructed is by far the most saturated complete genetic map of pepper, and using it we conducted fine QTL mapping for the important trait, FFN. QTLs and candidate genes obtained in this study lay a good foundation for the further research on FFN-related genes and other genetic applications in pepper.
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Affiliation(s)
- Xiao-fen Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
- College of Horticulture, China Agricultural University, Beijing, 100097 People’s Republic of China
| | - Guo-yun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Ting-ting Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Bin Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - He-shan Du
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Chang-bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Feng-lan Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Hai-ying Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Yong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Qian Wang
- College of Horticulture, China Agricultural University, Beijing, 100097 People’s Republic of China
| | - San-sheng Geng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
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Zhu Z, Sun B, Wei J, Cai W, Huang Z, Chen C, Cao B, Chen G, Lei J. Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits. Sci Rep 2019; 9:1054. [PMID: 30705330 PMCID: PMC6355862 DOI: 10.1038/s41598-018-38370-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/27/2018] [Indexed: 11/09/2022] Open
Abstract
The yield of pepper plants (Capsicum spp.) is their most important trait and is affected by the flower number and flowering time. Capsicum annuum produces a single flower per node and has an early flowering habit. By contrast, Capsicum chinense yields multiple flowers per node and has a late flowering character. However, the genetic mechanism underlying the control of these floral traits remains largely unknown. In this study, 150 F2 populations from an interspecific cross between the inbred lines 740 (C. chinense) and CA1 (C. annuum) and their parents were used to construct a molecular genetic linkage map using the specific length amplified fragment sequencing (SLAF-seq) technique. This linkage map, spanning 1,586.78 cM in length, contained 9,038 markers on 12 chromosomes, with a mean marker distance of 0.18 cM. Phenotypic data on the flowering time and flower number per node were collected over multiple years, and QTL analysis identified 6 QTLs for the flowering time and flower number per node by composite interval mapping (CIM) and genome-wide composite interval mapping (GCIM) methods at least in two environments. The candidate genes within the major QTL were predicted. In the major flowering time QTL, the candidate gene Capana02g000700, which encodes the homeotic protein APETALA2, was identified. Quantitative reverse-transcription PCR (qRT-PCR) analysis indicated that its expression level in 740 was higher than that in CA1. Gene expression analysis indicated that the expression of Capana02g000700 was significantly upregulated in flowers, and many floral development-related genes were found to be coexpressed with Capana02g000700, supporting the function of this gene in association with flowering time in C. chinense and C. annuum species.
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Affiliation(s)
- Zhangsheng Zhu
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Binmei Sun
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianlang Wei
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Cai
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhubin Huang
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Changming Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bihao Cao
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Guoju Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianjun Lei
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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21
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Wang G, Chen B, Du H, Zhang F, Zhang H, Wang Y, He H, Geng S, Zhang X. Genetic mapping of anthocyanin accumulation-related genes in pepper fruits using a combination of SLAF-seq and BSA. PLoS One 2018; 13:e0204690. [PMID: 30261055 PMCID: PMC6160195 DOI: 10.1371/journal.pone.0204690] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
Anthocyanins have significant functions in stress tolerance in pepper (Capsicum annuum L.) and also benefit human health. Nevertheless, the key structural genes and regulatory genes involved in anthocyanin accumulation in pepper fruits are still not well understood and fine mapped. For the present study, 383 F2 plants from a cross between the green-fruited C. annuum line Z5 and the purple-fruited line Z6 was developed. Two separate bulked DNA pools were constructed with DNAs extracted from either 37 plants with high anthocyanin content or from 18 plants with no anthocyanin. A combination of specific-locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was used to identify candidates for regions associated with anthocyanin accumulation. We identified a total of 127,004 high-quality single nucleotide polymorphism (SNP) markers, and detected 1674 high-quality SNP markers associated with anthocyanin accumulation. Three candidate anthocyanin-associated regions including the intervals from 12.48 to 20.00 Mb, from 54.67 to 56.59 Mb, and from 192.17 to 196.82 Mb were identified within a 14.10-Mb interval on chromosome 10 containing 126 candidate genes. Based on their annotations, we identified 12 candidate genes that are predicted to be associated with anthocyanin expression. The present results provide an efficient strategy for genetic mapping of and valuable insights into the genetic mechanisms of anthocyanin accumulation in pepper fruit, and allow us to clone and functionally analyze the genes that influence anthocyanin accumulation in this species.
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Affiliation(s)
- Guoyun Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Fenglan Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Haiying Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Yaqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Hongju He
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (XZ)
| | - Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (XZ)
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