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BMC Genomics ; 21(1): 141, 2020 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-32041544


BACKGROUND: Foxtail millet (Setaria italica) has been developed into a model genetical system for deciphering architectural evolution, C4 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. Thirty-nine 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 marker-assisted selection.

Front Genet ; 10: 1198, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31824578


Due to the maternal inheritance of cytoplasm, using foxtail millet [Setaria italica (L.) P. Beauv.] male sterile lines with a single cytoplasmic source as the female parent will inevitably lead to a narrow source of cytoplasm in hybrids, which may make them vulnerable to infection by cytoplasm-specific pathogens, ultimately leading to destructive yield losses. To assess cytoplasmic genetic diversity in plants, molecular markers derived from chloroplast DNA (cpDNA) have been used. However, such markers have not yet been applied to foxtail millet. In this study, we designed and screened nine pairs of polymorphic foxtail millet-specific primers based on its completely sequenced cpDNA. Using these primers, we analyzed the genetic diversity and cytoplasmic types of 130 elite foxtail millet parental lines collected in China. Our results revealed that the cytoplasmic genetic diversity of these accessions was low and needs to be increased. The parental lines were divided into four cytoplasmic types according to population structure analysis and a female parent-derivative evolutionary graph, indicating that the cytoplasmic types of elite foxtail millet lines were rather limited. A principal component analysis (PCA) plot was linked with the geographic and ecological distribution of accessions for each cytoplasmic type, as well as their basal maternal parents. Collectively, our results suggest that enriching cytoplasmic sources through the use of accessions from diverse ecological regions and other countries as the female parent may improve foxtail millet breeding programs, and prevent infection by cytoplasm-specific pathogens.

BMC Genomics ; 17: 336, 2016 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-27146360


BACKGROUND: Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundation for marker-assisted selection for agronomic traits and yield improvement. RESULT: A total of 10598 SSR markers were developed according to the reference genome sequence of foxtail millet cultivar 'Yugu1'. A total of 1013 SSR markers showing polymorphism between Yugu1 and Longgu7 were used to genotype 167 individuals from a Yugu1 × Longgu7 F2 population, and a high density genetic map was constructed. The genetic map contained 1035 loci and spanned 1318.8 cM with an average distance of 1.27 cM between adjacent markers. Based on agronomic and yield traits identified in 2 years, 29 QTL were identified for 11 traits with combined analysis and single environment analysis. These QTL explained from 7.0 to 14.3 % of phenotypic variation. Favorable QTL alleles for peduncle length originated from Longgu7 whereas favorable alleles for the other traits originated from Yugu1 except for qLMS6.1. CONCLUSIONS: New SSR markers, a high density genetic map and QTL identified for agronomic and yield traits lay the ground work for functional gene mapping, map-based cloning and marker-assisted selection in foxtail millet.

Mapeamento Cromossômico/métodos , Repetições de Microssatélites , Locos de Características Quantitativas , Setaria (Planta)/genética , China , Marcadores Genéticos , Genoma de Planta , Fenótipo , Filogenia , Análise de Sequência de DNA