Exploring Identity-By-Descent Segments and Putative Functions Using Different Foundation Parents in Maize

Wu, Xun; Li, Yongxiang; Fu, Junjie; Li, Xin; Li, Chunhui; Zhang, Dengfeng; Shi, Yunsu; Song, Yifu; Liu, Yu; Wang, Tianyu

doi:10.1371/journal.pone.0168374

Cited by 17 publications

(14 citation statements)

References 49 publications

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“…Based on a group of SNPs, a number of improvement‐selective sweeps involving a string of causal genes and IBD segments inherited from foundation parents have been identified, laying a foundation for germplasm resource analysis and breeding by design in the future. In recent years, an abundance studies have been performed to trace IBD segments and exploit key trait regions during the breeding process following their well‐defined genetic paths (Chen et al , ; Fang et al , ; Lai et al , ; Lu et al , ; Ma et al , ; Wu et al , ). Based on more than 2 million SNPs, the Xinjiang cotton population could be divided into two groups (Figure ), preliminarily indicating that Upland cotton populations in Xinjiang were not only spawned from DPL15, STV2B and UGDM, which are the original germplasms used for modern Upland cotton breeding in Yangtze River and Yellow River cotton‐growing regions in China (Fang et al , ), but also have a close kinship with the former Soviet Union cotton landraces.…”

Section: Discussionmentioning

confidence: 99%

“…These cultivars exhibit phenotypes commensurate with important traits (Shinada et al , ), as exemplified in the development of Kitaake, Kyowa and Huanghuazhan in rice (Shinada et al , ; Zhou et al , ), B73, Mo17, etc. in maize (Lai et al , ; Smith et al , ; Wu et al , ), and Ekangmian 9 and CRI12 in cotton (Lu et al , ; Ma et al , ). Moreover, identity‐by‐descent (IBD) regions have been demonstrated to be powerful in relatedness evaluation and mapping of genetic loci associated with phenotypic variations in many studies (Browning and Browning, ; Browning and Thompson, ; Stevens et al , ; Westerlind et al , ) .…”

Section: Introductionmentioning

confidence: 99%

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Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

Han

Qin

et al. 2020

Plant Biotechnology Journal

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Summary Xinjiang has been the largest and highest yield cotton production region not only in China, but also in the world. Improvements in Upland cotton cultivars in Xinjiang have occurred via pedigree selection and/or crossing of elite alleles from the former Soviet Union and other cotton producing regions of China. But it is unclear how genomic constitutions from foundation parents have been selected and inherited. Here, we deep‐sequenced seven historic foundation parents, comprising four cultivars introduced from the former Soviet Union (108Ф, C1470, 611Б and KK1543) and three from United States and Africa (DPL15, STV2B and UGDM), and re‐sequenced sixty‐nine Xinjiang modern cultivars. Phylogenetic analysis of more than 2 million high‐quality single nucleotide polymorphisms allowed their classification two groups, suggesting that Xinjiang Upland cotton cultivars were not only spawned from 108Ф, C1470, 611Б and KK1543, but also had a close kinship with DPL15, STV2B and UGDM. Notably, identity‐by‐descent (IBD) tracking demonstrated that the former Soviet Union cultivars have made a huge contribution to modern cultivar improvement in Xinjiang. A total of 156 selective sweeps were identified. Among them, apoptosis‐antagonizing transcription factor gene (GhAATF1) and mitochondrial transcription termination factor family protein gene (GhmTERF1) were highly involved in the determination of lint percentage. Additionally, the auxin response factor gene (GhARF3) located in inherited IBD segments from 108Ф and 611Б was highly correlated with fibre quality. These results provide an insight into the genomics of artificial selection for improving cotton production and facilitate next‐generation precision breeding of cotton and other crops.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

Han

Qin

et al. 2020

Plant Biotechnology Journal

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“…IBD segments can also be used to impute missing genotypes and infer haplotype phase (Kong et al., 2008). The combination of different IBD segments and genes could account for the formation of different FPs, and knowledge of IBD segments would provide extensive insight into the development of many more new candidate FP inbred lines in future maize breeding (Wu et al., 2016). Previous reports showed that most IBD segments were specific to particular FP subgroups.…”

Section: Introductionmentioning

confidence: 99%

“…Previous reports showed that most IBD segments were specific to particular FP subgroups. For example, Wu and colleagues reported that 116 IBD segments were specific to B73, 105 IBD segments were specific to Mo17, 111 IBD segments were specific to 207, and 190 IBD segments were specific to Huangzaosi (HZS; Wu et al., 2016). Liu and colleagues detected a total of 1,262, 1,373, and 1,019 IBD segments in the descendants of Dan340, Mo17, and HZS, respectively (Liu et al., 2015).…”

Section: Introductionmentioning

confidence: 99%

Dissection of identical‐by‐descent segments during the formation of foundation parents derived from Suwan germplasm of maize

Guo

et al. 2020

Plant Breeding

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Suwan germplasm plays important roles in maize breeding in tropical/subtropical regions, especially in southern China. To analyze the genetic characteristics of Suwan maize germplasm, one panel of 73 lines derived from the Suwan population and temperate resources were collected and genotyped using 56,110 single‐nucleotide polymorphism (SNP) markers. The results revealed four subgroups, namely, QR273, Ki32, HCL645, and PH4CV, with an average genetic distance of 0.304, varying from 0.001 to 0.370. In addition, many identical‐by‐descent (IBD) segments were found among Suwan germplasms and their descendants, of which 78 segments were detected only in the QR273 subgroup, 18 segments were detected only in the Ki32 subgroup, 53 and 11 segments were detected only in the PH4CV and the HCL645 subgroup, respectively. Pairwise comparisons showed that 13 segments were common between the QR273 and Ki32 subgroups, 5 segments were common between the QR273 and HCL645 subgroups, 26 segments were common between the QR273 and PH4CV subgroups. Five and 14 segments were common between the Ki32 versus HCL645 subgroups and Ki32 versus PH4CV subgroups. Three segments were commonly detected in the Ki32, QR273, and HCL645 subgroups. Candidate gene analysis showed that 132 genes were located in these segments, wherein seven new candidate genes were associated with flower time (FT)‐related traits, which were located in the IBD segments of QR273 or HCL645. Zm00001d033130_T005 and Zm00001d013768_T001 were located in the IBD segments specific to the QR273 subgroup. These two genes function in cell differentiation and flower development and would be very important for the phenotypic variations of the given FP subgroups. These results provide new insights and scientific proof for dissecting the genetic basis of complex traits and the utilization of Suwan germplasm in future maize breeding.

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“…Narrowing of ancestral composition in heterotic groups over time has resulted in significantly increased shared haplotype lengths in ex-PVPs compared to their predecessors Romay et al 2013). A few studies have identified specific segments of identity-by-state (IBS) haplotype sharing between a small number of founders and select maize inbreds (Dell'Acqua et al 2015;Jiao et al 2012;Romero-Severson et al 2001;Wu et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Haplotype structure in commercial maize breeding programs in relation to key founder lines

et al. 2019

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Haplotype structure in commercial maize breeding programs in relation to key Haplotype structure in commercial maize breeding programs in relation to key founder lines founder lines Abstract Abstract Key messageHigh-density haplotype analysis revealed significant haplotype sharing between ex-PVPs registered from 1976 to 1992 and key maize founders, and uncovered similarities and differences in haplotype sharing patterns by company and heterotic group. AbstractProprietary inbreds developed by the private seed industry have been the major source for driving genetic gain in successful North American maize hybrids for decades. Much of the history of industry germplasm can be traced back to key founder lines, some of which were pivotal in the development of prominent heterotic groups. Previous studies have summarized pedigree-based relationships, genetic diversity and population structure among commercial inbreds with expired Plant Variety Protection (ex-PVP). However, less is known about the extent of haplotype sharing between historical founders and ex-PVPs. A better understanding of the relationships between founders and ex-PVPs provides insight into the haplotype and heterotic group structure among industry germplasm. We performed high-density haplotype analysis with 11.3 million SNPs on 212 maize inbreds, which included 157 ex-PVPs registered 1976-1992 and 55 public lines relevant to PVPs. Among these lines were 12 key founders identified in literature review: 207, A632, B14, B37, B73, LH123HT, LH82, Mo17, Oh43, OH7, PHG39 and Wf9. Our results revealed that, on average, 81.6% of an ex-PVP's genome is shared with at least 1 of these 12 founder lines and more than half when limited to B73, Mo17 and 207. Quantifiable similarities and contrasts among heterotic groups and major US seed industry companies were also observed. The results from this study provide highresolution haplotype data on ex-PVP germplasm, confirm founder relationship trends observed in previous studies, uncover region-specific haplotype structure differences and demonstrate how haplotype sharing analysis can be used as a tool to explore germplasm diversity. Disciplines DisciplinesAgriculture | Agronomy and Crop Sciences | Ecology and Evolutionary Biology | Plant Breeding and Genetics Comments CommentsThis article is published as Coffman, Stephanie M., Matthew B. Hufford, Carson M. Andorf, and Thomas Lübberstedt. "Haplotype structure in commercial maize breeding programs in relation to key founder lines." Theoretical and Applied Genetics (2019). AbstractKey message High-density haplotype analysis revealed significant haplotype sharing between ex-PVPs registered from 1976 to 1992 and key maize founders, and uncovered similarities and differences in haplotype sharing patterns by company and heterotic group. Abstract Proprietary inbreds developed by the private seed industry have been the major source for driving genetic gain in successful North American maize hybrids for decades. Much of the history of industry germplasm can be traced back to key fou...

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Exploring Identity-By-Descent Segments and Putative Functions Using Different Foundation Parents in Maize

Cited by 17 publications

References 49 publications

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

Dissection of identical‐by‐descent segments during the formation of foundation parents derived from Suwan germplasm of maize

Haplotype structure in commercial maize breeding programs in relation to key founder lines

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