Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production

Thurber, Carrie S.; Ma, Justin M; Higgins, R. A.; Brown, Patrick J.

doi:10.1186/gb-2013-14-6-r68

Cited by 109 publications

(147 citation statements)

References 26 publications

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“…In the population studied here, it appears that alleles conditioning early flowering time are in coupling phase linkage with alleles conditioning smaller plant architecture and/or the traits are under positive pleiotropic control. Although the data set to which we have applied a statistical approach aiming to deduce the occurrence of direct unconscious selection may be underpowered, failure to reject the null hypothesis is consistent with tightly linked effects found for Ma1 in sorghum (Thurber et al, 2013) and pleiotropic effects found for Ghd7 in rice (Xue et al, 2008). In Hallauer's Tusón, there was secondary selection for reduced lodging, which could also explain some of the changes in PLH and ERH.…”

Section: Discussionmentioning

confidence: 94%

Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize

et al. 2014

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Crop species exhibit an astounding capacity for environmental adaptation, but genetic bottlenecks resulting from intense selection for adaptation and productivity can lead to a genetically vulnerable crop. Improving the genetic resiliency of temperate maize depends upon the use of tropical germplasm, which harbors a rich source of natural allelic diversity. Here, the adaptation process was studied in a tropical maize population subjected to 10 recurrent generations of directional selection for early flowering in a single temperate environment in Iowa, USA. We evaluated the response to this selection across a geographical range spanning from 43.05°(WI) to 18.00°(PR) latitude. The capacity for an all-tropical maize population to become adapted to a temperate environment was revealed in a marked fashion: on average, families from generation 10 flowered 20 days earlier than families in generation 0, with a nine-day separation between the latest generation 10 family and the earliest generation 0 family. Results suggest that adaptation was primarily due to selection on genetic main effects tailored to temperature-dependent plasticity in flowering time. Genotype-by-environment interactions represented a relatively small component of the phenotypic variation in flowering time, but were sufficient to produce a signature of localized adaptation that radiated latitudinally, in partial association with daylength and temperature, from the original location of selection. Furthermore, the original population exhibited a maladaptive syndrome including excessive ear and plant heights along with later flowering; this was reduced in frequency by selection for flowering time.

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Section: Discussionmentioning

confidence: 94%

Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize

et al. 2014

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“…Linkage disequilibrium between the most significant SNPs for Dw1 and SbFL9.1 is low, suggesting that they represent separate QTL rather than a single QTL with pleiotropic effects on plant height and flowering time (Thurber et al 2013). All joint linkage models for FL-IL that contain families B and C, in which the QTL appears to be segregating, identify the same SNP at 58.842 Mb (Figure 7).…”

Section: Resultsmentioning

confidence: 99%

Multiparental Mapping of Plant Height and Flowering Time QTL in Partially Isogenic Sorghum Families

Higgins

Thurber

Assaranurak

et al. 2014

G3 Genes|Genomes|Genetics

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Sorghum varieties suitable for grain production at temperate latitudes show dwarfism and photoperiod insensitivity, both of which are controlled by a small number of loci with large effects. We studied the genetic control of plant height and flowering time in five sorghum families (A–E), each derived from a cross between a tropical line and a partially isogenic line carrying introgressions derived from a common, temperate-adapted donor. A total of 724 F2:3 lines were phenotyped in temperate and tropical environments for plant height and flowering time and scored at 9139 SNPs using genotyping-by-sequencing. Biparental mapping was compared with multiparental mapping in different subsets of families (AB, ABC, ABCD, and ABCDE) using both a GWAS approach, which fit each QTL as a single effect across all families, and using a joint linkage approach, which fit QTL effects as nested within families. GWAS using all families (ABCDE) performed best at the cloned Dw3 locus, whereas joint linkage using all families performed best at the cloned Ma1 locus. Both multiparental approaches yielded apparently synthetic associations due to genetic heterogeneity and were highly dependent on the subset of families used. Comparison of all mapping approaches suggests that a GA2-oxidase underlies Dw1, and that a mir172a gene underlies a Dw1-linked flowering time QTL.

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“…Thus, sorghums bred in the USA prior to 1965 CE, and the photoperiod-insensitive alleles they encode (e.g., prr37 Milo , prr37 Kafir−2 ), were not dispersed outside the United States. Therefore, while the 'conversion' of tropical ecotypes markedly increased the diversity of temperatezone sorghum germplasm, introgression of dwarfism and day neutrality from a single donor inbred cultivar also created a genetic bottleneck at the genomic region spanning the PRR37 locus (Klein et al 2008;Thurber et al 2013). The purpose of the TAES-USDA Sorghum Conversion Program was to convert tropical sorghums to short-stature, early-flowering cultivars and to freely distribute 'converted' sorghums to seed companies and public breeding programs worldwide.…”

Section: Discussionmentioning

confidence: 99%

Allelic variants in the PRR37 gene and the human-mediated dispersal and diversification of sorghum

Klein

Miller²,

Dugas

et al. 2015

Theor Appl Genet

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Allele phylogenetic analysis of the sorghum flowering-time gene PRR37 provided new insight into the human-mediated selection of a key adaptive gene that occurred during sorghum's diversification and worldwide dispersal. The domestication and spread of the tropical cereal sorghum is associated with the historic movement of humans. We show that an allelic series at PRR37 (pseudo-response regulator 37), a circadian clock-associated transcription factor, was selected in long-day ecosystems worldwide to permit floral initiation and grain production. We identified a series of loss-of-function (photoperiod-insensitive) alleles encoding truncated PRR37 proteins, alleles with key amino acid substitutions in the pseudo-receiver domain, and a novel splice variant in which the pseudo-receiver domain is truncated. Each PRR37 allelic variant was traced to a specific geographic location or specialized agronomic type. We present a graphical model that shows evidence of human selection and gene flow of the PRR37 allelic variants during the global dispersal and agronomic diversification of sorghum. With the recent identification of the Ghd7 gene as an important regulator of flowering date in sorghum, we briefly examine whether loss-of-function Ghd7 allelic variants were selected prior to the human-mediated movement of sorghum from its equatorial center of origin to temperate climates worldwide.

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Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production

Cited by 109 publications

References 26 publications

Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize

Hallauer’s Tusón: a decade of selection for tropical-to-temperate phenological adaptation in maize

Multiparental Mapping of Plant Height and Flowering Time QTL in Partially Isogenic Sorghum Families

Allelic variants in the PRR37 gene and the human-mediated dispersal and diversification of sorghum

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