QTL mapping for 11 agronomic traits based on a genome-wide Bin-map in a large F2 population of foxtail millet (Setaria italica (L.) P. Beauv)

Wang, Zhilan; Wang, Jun; Peng, Jianxiang; Du, Xiaofen; Jiang, Maoshuang; Li, Yunfei; Han, Fang; Du, Guohua; Yang, Huiqing; Lian, Shichao; Yong, Jianpeng; Cai, Wei; Cui, Juduo; Han, Kangni; Yuan, Feng; Chang, Feng Ming; Yuan, Guobao; Zhang, Wenna; Zhang, Linyi; Peng, Shuzhong; Zou, Hong-Feng; Guo, Erhu

doi:10.1007/s11032-019-0930-6

Cited by 28 publications

(23 citation statements)

References 43 publications

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“…Since its domestication from green foxtail (Setaria viridis), foxtail millet has undergone a wide range of phenotypic changes in reduced vegetative branching, greater height, increased inflorescence branching and larger seeds (Hu et al 2018). Multiple studies have identified the genetic signatures of domestication and have highlighted genomic regions that harbored genes contributing to domestication-related traits (Doust et al 2004(Doust et al , 2005Jaiswal et al 2019;Jia et al 2013;Mauro-Herrera and Doust 2016;Mauro-Herrera et al 2013;Ni et al 2017;Wang et al 2017;Wang et al 2019;Yoshitsu et al 2017;Zhang et al 2017). Curiously, when orthologs of candidate domestication genes, such as Q (governing the free-threshing character in wheat), qsh1 (a major quantitative locus of seed shattering in rice), SH4 (responsible for the grain shattering in rice) and tb1 (responsible for the reduction of lateral branches in maize), were compared between foxtail millet and green foxtail, no coding differences were found, suggesting either that foxtail millet domestication employed a different set of loci or that genetic changes were not obvious by simple sequence scrutiny (Bennetzen et al 2012).…”

Section: Introductionmentioning

confidence: 99%

High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet

Wang

et al. 2021

Theor Appl Genet

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Key message Based on the high-density variation map, we identified genome-level evidence for local adaptation and demonstrated that Siprr37 with transposon insertion contributes to the fitness of foxtail millet in the northeastern ecoregion. Abstract Adaptation is a robust way through which plants are able to overcome environmental constraints. The mechanisms of adaptation in heterogeneous natural environments are largely unknown. Deciphering the genomic basis of local adaptation will contribute to further improvement in domesticated plants. To this end, we describe a high-depth (19.4 ×) haplotype map of 3.02 million single nucleotide polymorphisms in foxtail millet (Setaria italica) from whole-genome resequencing of 312 accessions. In the genome-wide scan, we identified a set of improvement signals (including the homologous gene of OsIPA1, a key gene controlling ideal plant architecture) related to the geographical adaptation to four ecoregions in China. In particular, based on the genome-wide association analysis results, we identified the contribution of a pseudo-response regulator gene, SiPRR37, to heading date adaptation in foxtail millet. We observed the expression changes of SiPRR37 resulted from a key Tc1–Mariner transposon insertion in the first intron. Positive selection analyses revealed that SiPRR37 mainly contributed to the adaptation of northeastern ecoregions. Taken together, foxtail millet adapted to the northeastern region by regulating the function of SiPRR37, which sheds lights on genome-level evidence for adaptive geographical divergence. Besides, our data provide a nearly complete catalog of genomic variation aiding the identification of functionally important variants.

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Section: Introductionmentioning

confidence: 99%

High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet

Wang

et al. 2021

Theor Appl Genet

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“…Its application value depends on the number of markers, the saturation of the map, and the uniformity of the distribution of markers on the map [25]. Therefore, a construction of a high-density linkage map could improve the accuracy of QTL mapping [27]. In recent years, with the development of sequencing technology and genome assemblies, SNP [12,26,27], SSR [16,29,30] [16] found similar results in the linkage map with 1013 SSRs markers constructed from F 2 population.…”

Section: A Novel High-density Linkage Mapmentioning

confidence: 95%

“…Therefore, a construction of a high-density linkage map could improve the accuracy of QTL mapping [27]. In recent years, with the development of sequencing technology and genome assemblies, SNP [12,26,27], SSR [16,29,30] [16] found similar results in the linkage map with 1013 SSRs markers constructed from F 2 population. However, the new map was constructed via RIL population with phenotypic stability, more markers (3413 bin markers), higher density (8.81 bin markers/Mb) and covered the whole genome.…”

Section: A Novel High-density Linkage Mapmentioning

confidence: 95%

“…Taking these results together, we deduced that was closely related to the accumulation of natural selection effect and the tighter linkage of chromosome fragment on SDRs as the number of self-crossing generation increases. [27]. Thus, they may be involved pleiotropic genes or closely linked alleles [16].…”

Section: Segregation Distortionmentioning

confidence: 99%

“…Wang et al [26] mapped 11 major QTLs of eight agronomic traits using RAD-seq to detect SNP markers and screen F 2 progenies derived from the cross between Hongmiaozhangu and Changnong35. In another study, Wang et al [27] identified 57 QTLs related to 11 agronomic traits in an F 2 mapping population from a cross between Aininghuang and Jingu21. These studies provided lots of information for genetic improvement and gene discovery.…”

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confidence: 99%

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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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Genomic Designing for Abiotic Stress Tolerance in Foxtail Millet (Setaria Italica L.)

Rana

Pramitha

Aggarwal

et al. 2021

Genomic Designing for Abiotic Stress Resistant Cereal Crops

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QTL mapping for 11 agronomic traits based on a genome-wide Bin-map in a large F2 population of foxtail millet (Setaria italica (L.) P. Beauv)

Cited by 28 publications

References 43 publications

High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet

High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet

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

Genomic Designing for Abiotic Stress Tolerance in Foxtail Millet (Setaria Italica L.)

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