Cytoplasmic male sterility (CMS) plays an important role in crop heterosis exploitation. Determining one or more nuclear genes that can restore male fertility to CMS is essential for developing hybrid cultivars. Genetic and physical mapping is the standard technique required for isolating these restoration genes. By screening 2,250 simple sequence repeat (SSR) primer pairs in cotton (Gossypium hirsutum L.), we identified five new SSR markers that are closely linked to the Rf1 gene, a fertility restorer gene of cotton for CMS-D2. Based on our previous fine mapping of the Rf1 gene and assemblage of three published STS markers, we constructed a high-resolution genetic map of Rf1 containing 13 markers in a genetic distance of 0.9 cM. The 13 molecular markers were used to screen a bacterial artificial chromosome (BAC) library from a restorer line 0-613-2R containing Rf1 gene, which yielded 50 single positive clones. There was an average of 3.8 clones ranging from 1 to 12 BAC clones per PCR marker. These 50 clones produced an average insert size of 120 kb (ranging between 80 and 225 kb). Thirty-five primer pairs were designed based on 38 sequences of BAC ends, and two new STS markers tightly linked to Rf1 gene have been tagged and integrated into this map. The physical map for the Rf1 gene was constructed by fingerprinting the positive clones digested with the HindIII enzyme. We were able to delimit the possible location of the Rf1 gene to a minimum of two BAC clones spanning an interval of approximately 100 kb between two clones designated 081-05K and 052-01N. Further work using these two BAC clones will lead to isolation of the Rf1 gene in cotton.
Because of the difficulty of producing F1 hybrid seeds by hand emasculation and pollination, wide use of heterosis in cotton production has been limited in China. The objective of this study was to evaluate the potential of F2 hybrids for yield and fibre quality. A half diallel involving eight parents and their F1 and F2 hybrids was grown in replicated studies at Linqing and Nanjing in 1999 and Nanjing in 2000. Yield and fibre quality was determined for all 64 entries. Fibre quality was also determined for parents and F1s, but only for Zhongmiansuo 28 (ZMS28), Xiangzamian 2 (XZM2) and Wanmian 13 (WM13) F2s. These three F2 hybrids are extensively planted in China and provide experimental controls with which to compare the performance of new hybrids. Average yield heterosis for F1s and F2s was 15.9 and 9.2%, respectively. Inbreeding depression for yield varied but some F2s greatly out‐yielded the best variety. Average F1 heterosis was 6.7, 6.2 and 2.9%, respectively for number of bolls per unit area, boll weight, and lint percentage. The average F2 heterosis for the same traits was 4.4, 3.3 and 1.6%, respectively. F1 heterosis for fibre traits was low. In general, parental average was a good indicator of the yield and fibre quality of F1 hybrids. These encouraging results suggest there is sufficient heterosis for yield to use F2s in China.
Dioscorea rotundata is an important food crop that is mainly cultivated in subtropical regions of the world. D. rotundata is frequently infected by various pathogens during its lifespan, which results in a substantial economic loss in terms of yield and quality. The disease resistance gene (R gene) profile of D. rotundata is largely unknown, which has greatly hampered molecular study of disease resistance in this species. Nucleotidebinding site-leucine-rich repeat (NBS-LRR) genes are the largest group of plant R genes, and they play important roles in plant defense responses to various pathogens. In this study, 167 NBS-LRR genes were identified from the D. rotundata genome. Subsequently, one gene was assigned to the resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) subclass and the other 166 genes to the coiled coil (CC)-NBS-LRR (CNL) subclass. None of the Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes were detected in the genome. Among them, 124 genes are located in 25 multigene clusters and 43 genes are singletons. Tandem duplication serves as the major force for the cluster arrangement of NBS-LRR genes. Segmental duplication was detected for 18 NBS-LRR genes, although no whole-genome duplication has been documented for the species. Phylogenetic analysis revealed that D. rotundata NBS-LRR genes share 15 ancestral lineages with Arabidopsis thaliana genes. The NBS-LRR gene number increased by more than a factor of 10 during D. rotundata evolution. A conservatively evolved ancestral lineage was identified from D. rotundata, which is orthologs to the Arabidopsis RPM1 gene. Transcriptome analysis for four different tissues of D. rotundata revealed a low expression of most NBS-LRR genes, with the tuber and leaf displaying a relatively high NBS-LRR gene expression than the stem and flower. Overall, this study provides a complete set of NBS-LRR genes for D. rotundata, which may serve as a fundamental resource for mining functional NBS-LRR genes against various pathogens.
Taro (Colocasia esculenta (L.), Schott), from the Araceae family, is one of the oldest crops with important edible, medicinal, nutritional and economic value. Taro is a highly polymorphic species including diverse genotypes adapted to a broad range of environments, but the taro genome has rarely been investigated. Here, a high‐quality chromosome‐level genome of C. esculenta was assembled using data sequenced by Illumina, PacBio and Nanopore platforms. The assembled genome size was 2,405 Mb with a contig N50 of 400.0 kb and a scaffold N50 of 159.4 Mb. In total, 2,311 Mb (96.09%) of the contig sequences was anchored onto 14 chromosomes to form pseudomolecules, and 2,126 Mb (88.43%) was annotated as repetitive sequences. Of the 28,695 predicted protein‐coding genes, 26,215 genes (91.4%) could be functionally annotated. On the basis of phylogenetic analysis using 769 genes, C. esculenta and Spirodela polyrhiza were placed on one branch of the tree that diverged approximately 73.23 million years ago. The synteny analyses showed that there have been two whole‐genome duplication events in C. esculenta separated by a relatively short gap. According to comparative genome analysis, a larger number (1,189) of distinct gene families and long terminal repeats were enriched in C. esculenta. Our high‐quality taro genome will provide valuable resources for further genetic, ecological and evolutionary analyses of taro or other species in the Araceae.
Taro (Colocasia esculenta. (L.) Schott) is a genus of perennial plants that is widely distributed in
A bacterial artificial chromosome (BAC) library containing a large genomic DNA insert is an important tool for genome physical mapping, map-based cloning, and genome sequencing. To isolate genes via a map-based cloning strategy and to perform physical mapping of the cotton genome, a high-quality BAC library containing large cotton DNA inserts is needed. We have developed a BAC library of the restoring line 0-613-2R for isolating the fertility restorer (Rf 1 ) gene and genomic research in cotton (Gossypium hirsutum L.). The BAC library contains 97 825 clones stored in 255 pieces of a 384-well microtiter plate. Random samples of BACs digested with the NotI enzyme indicated that the average insert size is approximately 130 kb, with a range of 80-275 kb, and 95.7% of the BAC clones in the library have an average insert size larger than 100 kb. Based on a cotton genome size of 2 250 Mb, library coverage is 5.7 × haploid genome equivalents. Four clones were selected randomly from the library to determine the stability of the BAC clones. There were no different fingerprints for 0 and 100 generations of each clone digested with NotI and HindIII enzymes. Thus, the stability of a single BAC clone can be sustained at least for 100 generations. Eight simple sequence repeat (SSR) markers flanking the Rf 1 gene were chosen to screen the BAC library by pool using PCR method and 25 positive clones were identified with 3.1 positive clones per SSR marker.
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