Development of a candidate gene marker for Rf 1 based on a PPR gene in cytoplasmic male sterile CMS-D2 Upland cotton

Wu, Jianyong; Cao, Xinde; Guo, Liping; Qi, Ting; Wang, Hailin; Tang, Huini; Zhang, Jinfa; Xing, Chaozhu

doi:10.1007/s11032-014-0032-4

Cited by 35 publications

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“…For example, in radish Rfo loci, three similar PPRs were identified, which may arise through gene duplication events [38]. In this study, five genes were not located on the Rf1 -carrying chromosome (Gh_D05), while the PPR gene Gh_D05G3392 is located on the chromosome where the restorer gene Rf1 resides [27], though it is outside of the Rf1 locus and its protein was predicted to target in the chloroplasts, and the physical distance is short. Therefore, we speculate that the Gh_D05G3392 gene may share a high similarity with Rf1 in cotton but it is not the candidate gene for Rf1 .…”

Section: Discussionmentioning

confidence: 95%

“…hirsutum and SSR marker GNCOT-C1-F (GenBank: KX090570.1). However, it is outside of the Rf1 locus [27], while other five genes were even not located on the Rf1 -carrying chromosome (Gh_D05). Thus, with the introduction of the dominant restorer gene Rf1 to the A line containing the CMS-inducing cytoplasm, the expression of the three PLS subfamily genes (PLS and E subgroup) was suppressed, while other three genes in the P subfamily were activated for male fertility restoration in the R line.…”

Section: Resultsmentioning

confidence: 99%

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A genome-wide identification and analysis of the DYW-deaminase genes in the pentatricopeptide repeat gene family in cotton (Gossypium spp.)

Zhang

Liu

et al. 2017

PLoS ONE

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The RNA editing occurring in plant organellar genomes mainly involves the change of cytidine to uridine. This process involves a deamination reaction, with cytidine deaminase as the catalyst. Pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain are reportedly associated with cytidine deamination, similar to members of the deaminase superfamily. PPR genes are involved in many cellular functions and biological processes including fertility restoration to cytoplasmic male sterility (CMS) in plants. In this study, we identified 227 and 211 DYW deaminase-coding PPR genes for the cultivated tetraploid cotton species G. hirsutum and G. barbadense (2n = 4x = 52), respectively, as well as 126 and 97 DYW deaminase-coding PPR genes in the ancestral diploid species G. raimondii and G. arboreum (2n = 26), respectively. The 227 G. hirsutum PPR genes were predicted to encode 52–2016 amino acids, 203 of which were mapped onto 26 chromosomes. Most DYW deaminase genes lacked introns, and their proteins were predicted to target the mitochondria or chloroplasts. Additionally, the DYW domain differed from the complete DYW deaminase domain, which contained part of the E domain and the entire E+ domain. The types and number of DYW tripeptides may have been influenced by evolutionary processes, with some tripeptides being lost. Furthermore, a gene ontology analysis revealed that DYW deaminase functions were mainly related to binding as well as hydrolase and transferase activities. The G. hirsutum DYW deaminase expression profiles varied among different cotton tissues and developmental stages, and no differentially expressed DYW deaminase-coding PPRs were directly associated with the male sterility and restoration in the CMS-D2 system. Our current study provides an important piece of information regarding the structural and evolutionary characteristics of Gossypium DYW-containing PPR genes coding for deaminases and will be useful for characterizing the DYW deaminase gene family in cotton biology and breeding.

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Section: Discussionmentioning

confidence: 95%

Section: Resultsmentioning

confidence: 99%

A genome-wide identification and analysis of the DYW-deaminase genes in the pentatricopeptide repeat gene family in cotton (Gossypium spp.)

Zhang

Liu

et al. 2017

PLoS ONE

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“…Yang et al [56] identi ed 6 EST-SSR markers (NAU2650, NAU2924, NAU3205, NAU3652, NAU3938, and NAU4040) with a genetic distance of 0.327 cM linked to Rf 1 of CMS-D2. Wu et al [20] screened 13 molecular markers closely linked to Rf 1 and located Rf 1 between the SSR markers BNL3535 and NAU3652, with a genetic distance of 0.049 cM and 0.078, respectively. Recently, they have reported co-segregated InDel markers such as InDel-1891, InDel-3434, InDel-7525, InDel-9356 and InDel-R [21,57].…”

Section: Molecular Marker Discovery and Ne Mapping Of The Fertility Rmentioning

confidence: 99%

“…The study of Yin et al [19] not only identi ed 5 new SSRs and 2 new STS markers for Rf 1 , but also made high-resolution genetic and physical maps of 15 markers at a genetic distance of 0.9 cM. More to this, Wu et al [20,21] recognized new BNL3535 SSR markers and developed 4 InDel markers by wholegenome resequencing. Zhao et al [22] used super-BSA and successfully mapped Rf 1 to 1.35 Mb region of chromosome D05.…”

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Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton

Feng

Zhang

et al. 2020

Preprint

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Background Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods The fertility of backcross population ((sterile line × restorer line) × maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. Selection of 24 SNPs through high-throughput genotyping and development InDel markers narrow down the candidate interval. The PPR genes and restore line up-regulated genes in the candidate interval were analyzed by RT-PCR. Results The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on Chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of previous anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions This study not only enabled us to precise locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.

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“…The restorer gene Rf 1 from the nuclear genome of D2‐2 can restore male fertility to both CMS‐D2 (Weaver and Weaver, 1977; Kohel et al, 1984; Zhang and Stewart, 2001b) and CMS‐D8 (Zhang and Stewart, 2001b), whereas Rf 2 from D8 only restores male fertility to CMS‐D8 (Zhang and Stewart, 2001b; Zhang et al, 2005). Both restorer genes were tightly linked on the same chromosome within a 1.0‐cM region on the basis of fertility segregation in a large testcross population (Zhang and Stewart, 2001b) and molecular linkage mapping (Liu et al, 2003; Zhang and Stewart, 2004; Feng et al, 2005; Yin et al, 2006; Wang et al, 2007, 2009; Wu et al, 2014, 2017b). In addition, the two CMS and restoration systems have been further characterized through DNA marker and gene expression analysis (Zhang et al, 2008; Wang et al, 2010; Wu et al, 2011, 2017a; Suzuki et al, 2013a, 2013b, 2013c; Yang et al, 2018).…”

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A Comparative Analysis of Cytoplasmic Effects on Lint Yield and Fiber Quality between CMS‐D2 and CMS‐D8 Systems in Upland Cotton

2019

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Hybrid vigor has been extensively used in crop production based on cytoplasmic male sterility (CMS). In upland cotton (Gossypium hirsutum L.), although CMS‐D2 has been extensively studied, the cytoplasmic effects of CMS‐D8 are currently unknown. The objectives of this study were to investigate the effects of CMS‐D8 cytoplasm using four pairs of reciprocal hybrids between a D8 restorer and four commercial cultivars, in comparison with another four pairs of reciprocal hybrids between a D2 restorer and the same cultivars. Across four crosses in four replicated field tests, the hybrids with D8 cytoplasm averaged 21% lower lint yield (LY), 10% lower lint percentage (LP), 7% lower boll weight (BW), and 11% lower micronaire (MIC) than their reciprocals with upland cytoplasm. However, the two groups of reciprocals had no overall difference for upper half mean length (UHML), uniformity index (UI), fiber bundle strength (STR), fiber elongation (ELO), and short fiber content (SFC). As a comparison, the four hybrids with D2 cytoplasm averaged 3 to 6% lower in LY, LP, BW, and ELO but improved UHML and STR by 7 to 8% and reduced MIC by 4% and SFC by 16% compared with their reciprocals with upland cytoplasm. However, D8 cytoplasm showed no significant negative effect on LY and LP in one test and on BW across the tests. It is concluded that the cytoplasmic effects from the two CMS systems are different, and CMS‐D8 presents a much greater challenge in reducing its large deleterious effects on LY before this CMS system can be used in commercial hybrid seed production.

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Development of a candidate gene marker for Rf 1 based on a PPR gene in cytoplasmic male sterile CMS-D2 Upland cotton

Cited by 35 publications

References 36 publications

A genome-wide identification and analysis of the DYW-deaminase genes in the pentatricopeptide repeat gene family in cotton (Gossypium spp.)

A genome-wide identification and analysis of the DYW-deaminase genes in the pentatricopeptide repeat gene family in cotton (Gossypium spp.)

Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton

A Comparative Analysis of Cytoplasmic Effects on Lint Yield and Fiber Quality between CMS‐D2 and CMS‐D8 Systems in Upland Cotton

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