Sweet Sorghum Originated through Selection of <i>Dry</i>, a Plant-Specific NAC Transcription Factor Gene

Zhang, Limin; Leng, Chuan-Yuan; Luo, Hong; Wu, Xiaoyuan; Liu, Zhiquan; Zhang, Yumiao; Zhang, Hong; Xia, Yan; Li, Shang; Liu, Chunming; Hao, Dongyun; Zhou, Yihua; Chu, Chengcai; Cai, Hongwei; Jing, Hai‐Chun

doi:10.1105/tpc.18.00313

Cited by 63 publications

(86 citation statements)

References 58 publications

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“…S13). The association on chromosome 6 is 433 kb from the classical D gene ( Sobic.006G147400 ) which has recently been cloned (Zhang et al, 2018; Xia et al, 2018; Fujimoto et al, 2018). The locus D was colocalized with the association (S6_50895868) for leaf midrib color (green vs. white) on chromosome 6 (Supplemental Fig.…”

Section: Resultsmentioning

confidence: 99%

An Integrated Genotyping‐by‐Sequencing Polymorphism Map for Over 10,000 Sorghum Genotypes

Olatoye

Marla

et al. 2019

The Plant Genome

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Core Ideas A reference single nucleotide polymorphism dataset covering over 10,000 sorghum genotypes was developed for the crop research community. The dataset was validated through gene‐resolution mapping of known genes for pigmentation, plant height, and flowering time. The value of the dataset was demonstrated with novel candidate genes for mesocarp thickness (Z), plant height (qPHT7.1), and other traits. Mining crop genomic variation can facilitate the genetic research of complex traits and molecular breeding. In sorghum [Sorghum bicolor L. (Moench)], several large‐scale single nucleotide polymorphism (SNP) datasets have been generated using genotyping‐by‐sequencing of ApeKI reduced representation libraries. However, data reuse has been impeded by differences in reference genome coordinates among datasets. To facilitate reuse of these data, we constructed and characterized an integrated 459,304‐SNP dataset for 10,323 sorghum genotypes on the version 3.1 reference genome. The SNP distribution showed high enrichment in subtelomeric chromosome arms and in genic regions (48% of SNPs) and was highly correlated (r = 0.82) to the distribution of ApeKI restriction sites. The genetic structure reflected population differences by botanical race, as well as familial structure among recombinant inbred lines (RILs). Faster linkage disequilibrium decay was observed in the diversity panel than in the RILs, as expected, given the greater opportunity for recombination in diverse populations. To validate the quality and utility of the integrated SNP dataset, we used genome‐wide association studies (GWAS) of genebank phenotype data, precisely mapping several known genes (e.g Y1 and Z) and identifying novel associations for other traits. We further validated the dataset with GWAS of new and published plant height and flowering time data in a nested association mapping population, precisely mapping known genes and identifying epistatic interactions underlying both traits. These findings validate this integrated SNP dataset as a useful genomics resource for sorghum genetics and breeding.

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Section: Resultsmentioning

confidence: 99%

An Integrated Genotyping‐by‐Sequencing Polymorphism Map for Over 10,000 Sorghum Genotypes

Olatoye

Marla

et al. 2019

The Plant Genome

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“…The location of genes in the lignin biosynthesis pathways that co-located with lodging QTL detected in this study are highlighted in green to the right of each chromosome, and those that did not co-locate with lodging QTL are highlighted in blue (Bout and Vermerris 2003; Saballos et al 2009, 2012, Sattler et al 2009, 2017, Walker et al 2013, 2016, Jun et al 2017, 2018; Wang et al 2017). The location of the recently cloned Dry gene is highlighted in red (Zhang et al 2018).…”

Section: Resultsmentioning

confidence: 99%

“…Based on phylogenetic relationships with functionally confirmed genes in sorghum and other species, predicted translational protein functions, enzymatic activity assay, and gene expression patterns, 21 candidate genes in the lignin biosynthesis pathways have been identified in sorghum (Bout and Vermerris, 2003; Jun et al , 2017, 2018, Saballos et al , 2012, 2009, Sattler et al , 2009, 2017, Walker et al , 2016, 2013; Wang et al , 2017). Additionally, the major morphological D gene, which changes the structure of the sorghum pith, was recently cloned (Zhang et al , 2018). Each of these genes was compared to the location of the QTL for lodging identified in this study.…”

Section: Resultsmentioning

confidence: 99%

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Large scale genome-wide association study reveals that drought induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

Wang

Mace

Tao

et al. 2019

Preprint

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Sorghum is generally grown in water limited conditions and often lodges under post-anthesis drought, which reduces yield and quality. Due to its complexity, our understanding on the genetic control of lodging is very limited. We dissected the genetic architecture of lodging in grain sorghum through genome-wide association study (GWAS) on 2308 unique hybrids grown in 17 Australian sorghum trials over 3 years. The GWAS detected 213 QTL, the majority of which showed a significant association with leaf senescence and plant height (72% and 71% respectively). Only 16 lodging QTL were not associated with either leaf senescence or plant height. The high incidence of multi-trait association for the lodging QTL indicates that lodging in grain sorghum is mainly associated with plant height and traits linked to carbohydrate remobilisation. This result supported the selection for stay-green (delayed leaf senescence) to reduce lodging susceptibility, rather than selection for short stature and lodging resistance per se, which likely reduces yield. Additionally, our data suggested a protective effect of stay-green on weakening the association between lodging susceptibility and plant height. Our study also showed that lodging resistance might be improved by selection for stem composition but was unlikely to be improved by selection for classical resistance to stalk rots.Key messageWe detected 213 lodging QTL and demonstrated that drought induced stem lodging in grain sorghum is substantially associated with stay-green and plant height, suggesting a critical role of carbon remobilisation.

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“…Tannin2 (Wu et al, 2019), Maturity6 ], many others are novel genes [e.g. Dwarf1 (Yamaguchi et al, 2016), Maturity2 (Casto et al, 2019), Dry (Zhang et al, 2018)].…”

Section: Candidate Genes For Plant Architecture Variationmentioning

confidence: 99%

Genome-wide mapping and prediction of plant architecture in a sorghum nested association mapping population

Olatoye

Morris

2020

Preprint

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Modifying plant architecture is often necessary for yield improvement and climate adaptation, but we lack understanding of the genotype-phenotype map for plant morphology in sorghum. Here, we use a nested association mapping (NAM) population that captures global allelic diversity of sorghum to characterize the genetics of leaf erectness, leaf width (at two stages), and stem diameter. Recombinant inbred lines (n = 2200) were phenotyped in multiple environments (35,200 observations) and joint linkage mapping was performed with ∼93,000 markers. Fifty-four QTL of small to large effect were identified for trait BLUPs (9–16 per trait) each explaining 0.4–4% of variation across the NAM population. While some of these QTL colocalize with sorghum homologs of grass genes [e.g. involved in hormone synthesis (maize spi1), floral transition (SbCN8), and transcriptional regulation of development (rice Ideal plant architecture1)], most QTL did not colocalize with an a priori candidate gene (82%). Genomic prediction accuracy was generally high in five-fold cross-validation (0.65–0.83), and varied from low to high in leave-one-family-out cross-validation (0.04–0.61). The findings provide a foundation to identify the molecular basis of architecture variation in sorghum and establish genomic-enabled breeding for improved plant architecture.Core ideasUnderstanding the genetics of plant architecture could facilitate the development of crop ideotypes for yield and adaptationThe genetics of plant architecture traits was characterized in sorghum using multi-environment phenotyping in a global nested association mapping populationFifty-five quantitative trait loci were identified; some colocalize with homologs of known developmental regulators but most do notGenomic prediction accuracy was consistently high in five-fold cross-validation, but accuracy varied considerably in leave-one-family-out predictions

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Sweet Sorghum Originated through Selection of Dry, a Plant-Specific NAC Transcription Factor Gene

Cited by 63 publications

References 58 publications

An Integrated Genotyping‐by‐Sequencing Polymorphism Map for Over 10,000 Sorghum Genotypes

An Integrated Genotyping‐by‐Sequencing Polymorphism Map for Over 10,000 Sorghum Genotypes

Large scale genome-wide association study reveals that drought induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

Genome-wide mapping and prediction of plant architecture in a sorghum nested association mapping population

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