Quantitative trait loci associated to agronomic traits and yield components in a &amp;lt;i&amp;gt;Sorghum bicolor&amp;lt;/i&amp;gt; L. Moench RIL population cultivated under pre-flowering drought and well-watered conditions

Phương, Nguyễn Thị Thu; Stützel, Hartmut; Uptmoor, Ralf

doi:10.4236/as.2013.412107

Cited by 19 publications

(18 citation statements)

References 22 publications

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“…Additionally, we identified one SNP aligning to sorghum chromosome 6 that was significantly associated with stem diameter when we corrected for the environmental influence of latitude. The stem diameter SNP was near two previously identified QTLs for stem diameter in sorghum (Shiringani et al, 2010;Phuong et al, 2013). We also identified one SNP on chromosome 3 that was significantly associated with stem height (corrected for latitude), and was near a previously identified sorghum QTL for plant height (Phuong et al, 2013).…”

Section: Snp-trait Associationssupporting

confidence: 54%

“…The stem diameter SNP was near two previously identified QTLs for stem diameter in sorghum (Shiringani et al, 2010;Phuong et al, 2013). We also identified one SNP on chromosome 3 that was significantly associated with stem height (corrected for latitude), and was near a previously identified sorghum QTL for plant height (Phuong et al, 2013). Heritability as estimated from SNP data was 0Á33, 0Á81 and 0Á71 for stems per area, stem height and stem diameter, respectively.…”

Section: Snp-trait Associationssupporting

confidence: 51%

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Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

Clark

Dzyubenko

et al. 2016

Ann Bot

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Background and aims Miscanthus is a genus of perennial C 4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. Âgiganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C 4 relatives maize, sorghum and sugarcane.Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites.Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43Á6 N) and on southern Sakhalin Island (46Á6 N). Miscanthus sacchariflorus was found inland at latitudes as high as 49Á3 N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0Á007 among diploid groups) but high genetic diversity (expected heterozygosity ¼ 0Á14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits.Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.

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Section: Snp-trait Associationssupporting

confidence: 54%

Section: Snp-trait Associationssupporting

confidence: 51%

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

Clark

Dzyubenko

et al. 2016

Ann Bot

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“…QTLs for grain yield in sorghum in combination with drought tolerance or cold tolerance or yield components (Kapanigowda et al, 2014;Nagaraja Reddy et al, 2013;Phuong et al, 2013;Rama Reddy et al, 2014;Sabadin et al, 2012). In addition, physiological parameters for leaf greenness (chlorophyll content and chlorophyll fluorescence) are reported to be positively correlated with grain yield under normal and drought conditions in wheat (Lopes and Reynolds, 2012;Pinto et al, 2010;Thomas and Smart, 1993) and sorghum (Harris et al, 2007;Xu et al, 2000a).…”

Section: Researchmentioning

confidence: 99%

QTL Mapping for Grain Yield, Flowering Time, and Stay‐Green Traits in Sorghum with Genotyping‐by‐Sequencing Markers

Sukumaran

Zhu

et al. 2016

Crop Science

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Molecular breeding can complement traditional breeding approaches to achieve genetic gains in a more efficient way. In the present study, genetic mapping was conducted in a sorghum recombinant inbred line (RIL) population developed from Tx436 (a non‐stay‐green high food quality inbred) × 00MN7645 (a stay‐green high yield inbred) and evaluated in eight environments (location and year combination) in a hybrid background of Tx3042 (a non‐stay‐green A‐line). Phenotyping was conducted for agronomic traits (grain yield and flowering time), physiological traits of stay‐green (chlorophyll content [SPAD] and chlorophyll fluorescence [Fv/Fm] measured on the leaves), and green leaf area visual score (GLAVS). This population was genotyped with genotyping‐by‐sequencing (GBS) technology. Data processing resulted in 7144 high quality single nucleotide polymorphisms (SNPs) that were used in a genome‐wide single marker scan with physical distance. A selected subset of 1414 SNPs was used for composite interval mapping (CIM) with genetic distance. These complementary methods revealed fifteen QTLs for the traits studied. In addition, QTL mapping for individual environments and year‐wise combinations revealed 42 QTLs. A consistent QTL for grain yield under normal and stressed conditions was identified in chromosome 1 that explained 8 to 16% of the phenotypic variation. QTLs for flowering time were identified in chromosomes 2, 6, and 9 that explained 6 to 11% of the phenotypic variation. Stay‐green QTLs in chromosomes 3 and 4 explained 8 to 24% of the phenotypic variation. These identified QTLs with flanking SNPs of known genomic positions could be used to improve grain yield, flowering time, and stay‐green in sorghum molecular breeding programs.

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“…Given the conservation of gene function among closely related cereal species, this presents opportunities for comparative genomics studies to investigate the genetics of grain size in other cereal crops using knowledge gained from gene cloning studies in maize and rice. The sorghum QTL atlas of Mace et al () details around 100 grain weight QTL in sorghum that have been identified through linkage analysis in 18 studies (Bai et al , ; Boyles et al , ; Brown et al , ; Feltus et al , ; Gelli et al , ; Han et al , ; Mocoeur et al , ; Murray et al , ; Paterson et al , ; Phuong et al , ; Rajkumar et al , ; Rami et al , ; Reddy et al , ; Shehzad and Okuno, ; Spagnolli et al , ; Srinivas et al , ; Tao et al , ; Tuinstra et al , ). A further 12 markers associated with grain weight have been identified in three GWAS studies (Boyles et al , ; Upadhyaya et al , ; Zhang et al , ).…”

Section: Introductionmentioning

confidence: 99%

Large‐scale GWAS in sorghum reveals common genetic control of grain size among cereals

Tao

Zhao

Wang

et al. 2019

Plant Biotechnology Journal

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Summary Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype’s genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome‐wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC‐NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype’s capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.

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Quantitative trait loci associated to agronomic traits and yield components in a <i>Sorghum bicolor</i> L. Moench RIL population cultivated under pre-flowering drought and well-watered conditions

Cited by 19 publications

References 22 publications

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

QTL Mapping for Grain Yield, Flowering Time, and Stay‐Green Traits in Sorghum with Genotyping‐by‐Sequencing Markers

Large‐scale GWAS in sorghum reveals common genetic control of grain size among cereals

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