Updated foxtail millet genome assembly and gene mapping of nine key agronomic traits by resequencing a RIL population

Ni, Xiliang; Xia, Qiuju; Zhang, Houbao; Cheng, Shu; Li, Hui; Fan, Guangyu; Guo, Tao; Huang, Ping; Xiang, Haitao; Chen, Qingchun; Li, Ning; Zou, Hong-Feng; Cai, Xuemei; Lei, Xuejing; Wang, Xiaoming; Zhou, Chengshu; Zhao, Zhihai; Zhang, Gengyun; Du, Guohua; Cai, Wei; Quan, Zhiwu

doi:10.1093/gigascience/giw005

Cited by 33 publications

(28 citation statements)

References 24 publications

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“…closely related to bio-fuel grasses such as switchgrass and Napier grass [73,74]. Hence, we suggest that the results presented here have implications in understanding the response of other important crops.…”

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confidence: 66%

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions

et al. 2020

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Food insecurity is a looming threat for the burgeoning world population. Phosphorus (P), which is absorbed from soil as inorganic phosphate (Pi), is an essential macronutrient for the growth of all agricultural crops. This study reports phenotype analysis for P responses in natural field and greenhouse conditions, using 54 genotypes of foxtail millet (Setaria italica) representing wide geographic origins. The genotype responses were assessed in natural field conditions in two different seasons (monsoon and summer) under Pi-fertilized (P+) and unfertilized (P-) soil for eight above-ground traits. Enormous variations were seen among the genotypes in phenotypic responses for all the measured parameters under low P stress conditions. Variations were significant for plant height, leaf number and length, tillering ability and seed yield traits. Genotypes ISe 1234 and ISe 1541 were P+ responders, and the genotypes ISe 1181, ISe 1655, ISe 783 and ISe 1892 showed tolerance to low P for total seed yield. Genotypes that performed well under P-conditions were almost as productive as genotypes that performed well under P+ conditions suggesting some genotypes are well adapted to nutrient-poor soils. In the greenhouse, most of the genotypes produced changes in root architecture that are characteristic of P-stress, but to differing degrees. Significant variation was seen in root hair density and root hair number and in fresh and dry weight of shoot and root under P-stress. However, there was not much difference in the shoot and root total P and Pi levels of five selected high and low responding genotypes. We noticed contrasting responses in the greenhouse and natural field experiments for most of these genotypes. The leads from the study form the basis for breeding and improvement of foxtail millet for better Pi-use efficiency.

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confidence: 66%

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions

et al. 2020

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“…In recent years, whole-genome re-sequencing technology has been widely used in population genetic analysis [24][25][26]. The high-throughput genotyping platform of SNP markers has significantly driven the process of genetic mapping and QTL identification [27][28][29]. Compared with the low density of traditional molecular markers, SNP markers significantly improve the genome coverage and QTL mapping accuracy.…”

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confidence: 99%

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

Zhu

Wang

et al. 2020

BMC Genomics

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Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

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“…Five hundred and twelve loci associated with 47 agronomic traits were identified through genome wide association studies (GWAS). Ni et al [24] and Zhang et al [25] resequenced a RIL population using single seed descent strategy from a cross between Zhanggu and A2, and developed a high-resolution bin map with high-density SNP markers. A total of 69 QTLs for 21 agronomic traits were identified.…”

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confidence: 99%

QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica)

Liu

Dong

et al. 2020

BMC Genomics

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Background: Foxtail millet (Setaria italica) has been developed into a model genetical system for deciphering architectural evolution, C 4 photosynthesis, nutritional properties, abiotic tolerance and bioenergy in cereal grasses because of its advantageous characters with the small genome size, self-fertilization, short growing cycle, small growth stature, efficient genetic transformation and abundant diverse germplasm resources. Therefore, excavating QTLs of yield component traits, which are closely related to aspects mentioned above, will further facilitate genetic research in foxtail millet and close cereal species. Results: Here, 164 Recombinant inbreed lines from a cross between Longgu7 and Yugu1 were created and 1,047, 978 SNPs were identified between both parents via resequencing. A total of 3413 bin markers developed from SNPs were used to construct a binary map, containing 3963 recombinant breakpoints and totaling 1222.26 cM with an average distance of 0.36 cM between adjacent markers. Forty-seven QTLs were identified for four traits of straw weight, panicle weight, grain weight per plant and 1000-grain weight. These QTLs explained 5.5-14.7% of phenotypic variance. Thirtynine favorable QTL alleles were found to inherit from Yugu1. Three stable QTLs were detected in multi-environments, and nine QTL clusters were identified on Chromosome 3, 6, 7 and 9.Conclusions: A high-density genetic map with 3413 bin markers was constructed and three stable QTLs and 9 QTL clusters for yield component traits were identified. The results laid a powerful foundation for fine mapping, identifying candidate genes, elaborating molecular mechanisms and application in foxtail millet breeding programs by markerassisted selection.

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Updated foxtail millet genome assembly and gene mapping of nine key agronomic traits by resequencing a RIL population

Cited by 33 publications

References 24 publications

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica)

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