QTL detection for wheat kernel size and quality and the responses of these traits to low nitrogen stress

Cui, Fa; Fan, Xiangtao; Chen, Mei; Zhang, Na; Zhao, Chunhua; Zhang, Wei; Han, Jie; Ji, Jun; Zhao, Xueqiang; Yang, Lijuan; Zhao, Zhihui; Tong, Yiping; Wang, Tao; Li, Junming

doi:10.1007/s00122-015-2641-7

Cited by 88 publications

(78 citation statements)

References 63 publications

(119 reference statements)

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“…Similarly, Maccaferri et al [6] identified one MTA on 7AL and 7BL in durum wheat. MTAs on chromosomes 7 have been also found in bread wheat [68, 86] and in a mapping population from wild emmer and durum wheat [46, 54]. It is remarkable that the QTLs conferring improved TKW on chromosome 7B have been co-localized with QTLs conferring higher grain yield [46].…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Association Mapping for Agromorphological and Grain Quality Traits of a Structured Collection of Durum Wheat Landraces Including subsp. durum, turgidum and diccocon

Giraldo

Royo²,

González³

et al. 2016

PLoS ONE

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Association mapping was performed for 18 agromorphological and grain quality traits in a set of 183 Spanish landraces, including subspecies durum, turgidum and dicoccon, genotyped with 749 DArT (Diversity Array Technology) markers. Large genetic and phenotypic variability was detected, being the level of diversity among the chromosomes and genomes heterogeneous, and sometimes complementary, among subspecies. Overall, 356 were monomorphic in at least one subspecies, mainly in dicoccon, and some of them coincidental between subspecies, especially between turgidum and dicoccon. Several of those fixed markers were associated to plant responses to environmental stresses or linked to genes subjected to selection during tetraploid wheat domestication process. A total of 85 stable MTAs (marker–trait associations) have been identified for the agromorphological and quality parameters, some of them common among subspecies and others subspecies-specific. For all the traits, we have found MTAs explaining more than 10% of the phenotypic variation in any of the three subspecies. The number of MTAs on the B genome exceeded that on the A genome in subsp. durum, equalled in turgidum and was below in dicoccon. The validation of several adaptive and quality trait MTAs by combining the association mapping with an analysis of the signature of selection, identifying the putative gene function of the marker, or by coincidences with previous reports, showed that our approach was successful for the detection of MTAs and the high potential of the collection to identify marker–trait associations. Novel MTAs not previously reported, some of them subspecies specific, have been described and provide new information about the genetic control of complex traits.

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Section: Discussionmentioning

confidence: 99%

Genetic Diversity and Association Mapping for Agromorphological and Grain Quality Traits of a Structured Collection of Durum Wheat Landraces Including subsp. durum, turgidum and diccocon

Giraldo

Royo²,

González³

et al. 2016

PLoS ONE

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“…The nitrogen treatments, field arrangements and experimental designs of the ten environments were performed as described previously 3, 68, 69 .…”

Section: Methodsmentioning

confidence: 99%

Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number

Cui

Zhang

Fan

et al. 2017

Sci Rep

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211

121

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In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.High-density genetic linkage maps are essential for genetic and genomic research in crops 1-4 . Molecular breeding is more effective if the molecular map is dense to provide more choices in the quality and type of markers and to increase the probability of detecting polymorphic markers in important chromosomal intervals. In wheat, the large genome size (17 gigabases), hexaploid nature (AABBDD), high percentage of repetitive regions and low level of polymorphism have complicated the acquisition of high-resolution genetic maps by molecular markers 1-4 . To date, several kinds of molecular markers, including restriction fragment length polymorphism (RFLP) 5,6 , amplified fragment length polymorphism (AFLP) 7 , simple sequence repeats (SSRs) 8,9 , and diversity array technology (DArT) 3, 4, 10, 11 have been used to construct genetic linkage maps in wheat. Information regarding wheat molecular markers and genetic maps is available in some datasets such as GrainGenes 2.0 (https:// wheat.pw.usda.gov/GG3/), URGI (https://urgi.versailles.inra.fr/), etc. Most of these markers are mapped on the telomeric regions, and there is very limited map resolution in proximal part of the chromosomes 3 . Therefore, the density and coverage of the current genetic maps are less than satisfactory.Single-nucleotide polymorphisms (SNPs) are the most abundant type of molecular marker. Accurate and reliable methods have been developed to perform high-throughput genotyping based on SNPs 12 . With the development of new sequencing technologies, increasing numbers of SNPs have been discovered in wheat 1, 2, 13-15 .

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“…Suggestive QTLs with an average LOD value >3.0 in a dataset were noted. A QTL with an average LOD value > 3.0 and average phenotypic variance contribution > 10% was defined as a major QTL [55,56]. The QTLs in the present study were compared with previously published ones [2,21,31,32].…”

Section: Linkage Mapmentioning

confidence: 98%

Identification and Validation of Candidate Genes Conferring Resistance to Downy Mildew in Maize (Zea mays L.)

Kim

Song

et al. 2020

Genes

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Downy mildew (DM) is a major disease of maize that causes significant yield loss in subtropical and tropical regions around the world. A variety of DM strains have been reported, and the resistance to them is polygenically controlled. In this study, we analyzed the quantitative trait loci (QTLs) involved in resistance to Peronosclerospora sorghi (sorghum DM), P. maydis (Java DM), and Sclerophthora macrospora (crazy top DM) using a recombinant inbred line (RIL) from a cross between B73 (susceptible) and Ki11 (resistant), and the candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were discovered. The linkage map was constructed with 234 simple sequence repeat (SSR) and restriction fragment length polymorphism (RFLP) markers, which was identified seven QTLs (chromosomes 2, 3, 6, and 9) for three DM strains. The major QTL, located on chromosome 2, consists of 12.95% of phenotypic variation explained (PVE) and a logarithm of odds (LOD) score of 14.12. Sixty-two candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were obtained between the flanked markers in the QTL regions. The relative expression level of candidate genes was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) using resistant (CML228, Ki3, and Ki11) and susceptible (B73 and CML270) genotypes. For the 62 candidate genes, 15 genes were upregulated in resistant genotypes. Among these, three (GRMZM2G028643, GRMZM2G128315, and GRMZM2G330907) and AC210003.2_FG004 were annotated as leucine-rich repeat (LRR) and peroxidase (POX) genes, respectively. These candidate genes in the QTL regions provide valuable information for further studies related to P. sorghi, P. maydis, and S. macrospora resistance.Genes 2020, 11, 191 2 of 20 is spread by oospores that survive in the soil [7] and can be spread through infected seeds or from plant-to-plant by airborne conidia. Because of the systemic nature of DM, susceptible lines usually die when infected in the seedling emergence stage, and when plants are infected during later growth stages, they cannot develop the maize ear despite having survived. At least six pathogens that cause DM infection of maize in Asia have been reported, including sorghum DM (P. sorghi (Weston & Uppal)), Philippine DM (P. philippinensis (Weston) Shaw), Java DM (P. maydis (Raciborski)), sugarcane DM (P. sacchari (Miyabe) Shirai and Hara), brown stripe DM (Sclerophthora rayssiae var. zeae), crazy top DM (S. macrospora), and Rajasthan DM (P. heteropogoni) [2,6,[8][9][10][11][12][13][14][15]. DM is widespread in tropical regions, although its origin is conjectural, and because of the diversity of the DM pathogens and their systemic nature, the development of resistant varieties is needed. Moreover, a renewed emphasis on cost-effectiveness and environmental safety that has brought about the application of DM management by the development of resistant varieties. According to studies on the interaction of maize and the pathogens, resistance to DM is polygenically controlled [7,13,[16][17][18]...

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QTL detection for wheat kernel size and quality and the responses of these traits to low nitrogen stress

Cited by 88 publications

References 63 publications

Genetic Diversity and Association Mapping for Agromorphological and Grain Quality Traits of a Structured Collection of Durum Wheat Landraces Including subsp. durum, turgidum and diccocon

Genetic Diversity and Association Mapping for Agromorphological and Grain Quality Traits of a Structured Collection of Durum Wheat Landraces Including subsp. durum, turgidum and diccocon

Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number

Identification and Validation of Candidate Genes Conferring Resistance to Downy Mildew in Maize (Zea mays L.)

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