scholarly journals Unlocking the relationships among population structure, plant architecture, growing season, and environmental adaptation in Henan wheat cultivars

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Jian Yang ◽  
Yanjie Zhou ◽  
Weiguo Hu ◽  
Yu’e Zhang ◽  
Yong Zhou ◽  
...  
Keyword(s):  
Grain Yield ◽  
Plant Architecture ◽  
Selective Sweep ◽  
Association Studies ◽  
Growing Season ◽  
Kernel Weight ◽  
High Yield ◽  
Population Divergence ◽  
Genome Wide Association Studies ◽  
Wheat Cultivars

Abstract Background Ecological environments shape plant architecture and alter the growing season, which provides the basis for wheat genetic improvement. Therefore, understanding the genetic basis of grain yield and yield-related traits in specific ecological environments is important. Results A structured panel of 96 elite wheat cultivars grown in the High-yield zone of Henan province in China was genotyped using an Illumina iSelect 90 K SNP assay. Selection pressure derived from ecological environments of mountain front and plain region provided the initial impetus for population divergence. This determined the dominant traits in two subpopulations (spike number and spike percentage were dominance in subpopulation 2:1; thousand-kernel weight, grain filling rate (GFR), maturity date (MD), and fertility period (FP) were dominance in subpopulation 2:2), which was also consistent with their inheritance from the donor parents. Genome wide association studies identified 107 significant SNPs for 12 yield-related traits and 10 regions were pleiotropic to multiple traits. Especially, GY was co-located with MD/FP, GFR and HD at QTL-ple5A, QTL-ple7A.1 and QTL-ple7B.1 region. Further selective sweep analysis revealled that regions under selection were around QTLs for these traits. Especially, grain yield (GY) is positively correlated with MD/FP and they were co-located at the VRN-1A locus. Besides, a selective sweep signal was detected at VRN-1B locus which was only significance to MD/FP. Conclusions The results indicated that extensive differential in allele frequency driven by ecological selection has shaped plant architecture and growing season during yield improvement. The QTLs for yield and yield components detected in this study probably be selectively applied in molecular breeding.

scholarly journals Genome-wide association studies on heat stress tolerance during grain development in wheat (Triticum aestivum L.)

2020 ◽  
Author(s):  
Jie Guo ◽  
Weiping Shi ◽  
Jiahui Guo ◽  
Linqi Yue ◽  
Lei Zhuang ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Tolerance ◽  
Association Studies ◽  
Starch Content ◽  
Kernel Weight ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Genome Wide Association Studies ◽  
Wheat Cultivars ◽  
Genome Wide

Abstract BackgroundHeat stress at the late reproductive stages is a common problem encountered in autumn-sown wheat production regions in China with the affected area covering as much as two-thirds of the crop. In order to develop wheat cultivars with heat-tolerance, it is crucial to explore favorable alleles for use in breeding programs.ResultsIn this study, we performed a 90K iSelect SNP genotyping assay on a collection of 207 wheat cultivars subjected to heat stress during grain-fill growth stage in three years (2015-2017). Genotypic analyses of 19 phenotypic traits revealed that heat stress had major impacts on grain weight, size, and quality. Correlation analyses indicated that thousand kernel weight (TKW) was significantly correlated with grain width (GW) and grain perimeter (GP), whereas grain protein content (GPC) was negatively correlated with total starch content (TSC) (P <0.01). We applied heat susceptibility indices (HSI) for different traits to assess heat tolerance. Genome-wide association studies (GWAS) revealed a total of 125 marker-trait associations (MTAs) at 63 SNP loci on 16 chromosomes each accounting for phenotypic variation (R2) of 3.0-21.4%. 17 loci showed significant associations in three environments. The analysis of selective sweeps indicated that RAC875_c19042_2102 (2B), wsnp_Ex_c257_491667 (3B), wsnp_Ex_rep_c101323_86702413 (5A) and BS00061911_51 (7A) were selected between two subpopulations (top 5%).ConclusionsThese four key MTAs detected in the present study are candidates for further genetic dissection and development of molecular markers.

scholarly journals Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251745
Author(s):  
Caléo Panhoca de Almeida ◽  
Jean Fausto de Carvalho Paulino ◽  
Caio Cesar Ferrari Barbosa ◽  
Gabriel de Moraes Cunha Gonçalves ◽  
Roberto Fritsche-Neto ◽  
...  
Keyword(s):  
Quantitative Resistance ◽  
Association Studies ◽  
Colletotrichum Lindemuthianum ◽  
Genome Wide Association ◽  
High Yield ◽  
Genome Wide Association Studies ◽  
Anthracnose Resistance ◽  
Resistant Cultivars ◽  
Genome Wide ◽  
Selection Of

Brazil is the largest consumer of dry edible beans (Phaseolus vulgaris L.) in the world, 70% of consumption is of the carioca variety. Although the variety has high yield, it is susceptible to several diseases, among them, anthracnose (ANT) can lead to losses of up to 100% of production. The most effective strategy to overcome ANT, a disease caused by the fungus Colletotrichum lindemuthianum, is the development of resistant cultivars. For that reason, the selection of carioca genotypes resistant to multiple ANT races and the identification of loci/markers associated with genetic resistance are extremely important for the genetic breeding process. Using a carioca diversity panel (CDP) with 125 genotypes and genotyped by BeadChip BARCBean6K_3 and a carioca segregating population AM (AND-277 × IAC-Milênio) genotyped by sequencing (GBS). Multiple interval mapping (MIM) and genome-wide association studies (GWAS) were used as mapping tools for the resistance genes to the major ANT physiological races present in the country. In general, 14 single nucleotide polymorphisms (SNPs) showed high significance for resistance by GWAS, and loci associated with multiple races were also identified, as the Co-3 locus. The SNPs ss715642306 and ss715649427 in linkage disequilibrium (LD) at the beginning of chromosome Pv04 were associated with all the races used, and 16 genes known to be related to plant immunity were identified in this region. Using the resistant cultivars and the markers associated with significant quantitative resistance loci (QRL), discriminant analysis of principal components (DAPC) was performed considering the allelic contribution to resistance. Through the DAPC clustering, cultivar sources with high potential for durable anthracnose resistance were recommended. The MIM confirmed the presence of the Co-14 locus in the AND-277 cultivar which revealed that it was the only one associated with resistance to ANT race 81. Three other loci were associated with race 81 on chromosomes Pv03, Pv10, and Pv11. This is the first study to identify new resistance loci in the AND-277 cultivar. Finally, the same Co-14 locus was also significant for the CDP at the end of Pv01. The new SNPs identified, especially those associated with more than one race, present great potential for use in marker-assisted and early selection of inbred lines.

scholarly journals GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2048
Author(s):  
Liyuan Liu ◽  
Jinghang Zhou ◽  
Chunpeng James Chen ◽  
Juan Zhang ◽  
Wan Wen ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Milk Yield ◽  
Milk Fat ◽  
Association Studies ◽  
High Yield ◽  
Holstein Cattle ◽  
Genome Wide Association Studies ◽  
Genetic Loci ◽  
Breeding Values ◽  
Genome Wide

High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and quality traits in Holstein cattle population from China. These traits included milk yield, fat, and protein. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a linear mixed model. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten single-nucleotide polymorphisms (SNPs) were detected above the genome-wide significant threshold (p < 4.0 × 10−7), including six located in previously reported quantitative traits locus (QTL) regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The study not only identified the effect of DGAT1 gene on milk fat and protein, but also discovered novel genetic loci and candidate genes related to milk traits. These novel genetic loci would be an important basis for molecular breeding in dairy cattle.

scholarly journals Genome‐Wide Association Studies of Grain Yield Components in Diverse Sorghum Germplasm

2016 ◽  
Vol 9 (2) ◽  
Author(s):  
Richard E. Boyles ◽  
Elizabeth A. Cooper ◽  
Matthew T. Myers ◽  
Zachary Brenton ◽  
Bradley L. Rauh ◽  
...  
Keyword(s):  
Grain Yield ◽  
Yield Components ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Grain Yield Components ◽  
Sorghum Germplasm

Production and survival of tillers of wheat and their contribution to yield

1974 ◽  
Vol 83 (1) ◽  
pp. 117-124 ◽  
Author(s):  
H. M. Ishag ◽  
M. B. Taha
Keyword(s):  
Grain Yield ◽  
Air Temperature ◽  
High Mortality ◽  
Growth Period ◽  
Dry Weight ◽  
Growing Season ◽  
Sowing Date ◽  
Wheat Cultivars ◽  
Nitrogen Application ◽  
True Leaf

SUMMARYThe effect of sowing date and nitrogen on tillering patterns, survival and contribution of reproductive tillers to grain yield of standard and Mexican wheat cultivars were studied for two seasons.Maximum number of tillers/plant, 3·2–4·5, was observed after 40 and 27 days from sowing for 1970–1 and 1971–2 respectively. The number of ears/plant was 1·4 at the end of the growing season. Varieties differed in tillering, and LRN10 and Giza 155 produced more reproductive tillers than Falchetto and Mexipak. Nitrogen application increased tillering efficiency, i.e. ratio of fertile to total tillers produced. Only 26% of tillers appearing in the axil of the first true leaf (T1) and 10% of tillers in the axil of the second true leaf (T2) survived to produce ears. The high mortality of tillers was attributed to high air temperature prevailing during the growth period (33 °C by day; 18 °C by night). Eared tillers did not die and were self supporting because of the photosynthesis by the ear.Grain weight/tiller was positively correlated with tiller dry weight at heading, r= 0·76–0·96. Main shoots contributed about 81% of the total grain yield and 19% came from T1 and T2 tillers.

Responsiveness of barley cultivars to nitrogen fertiliser

1997 ◽  
Vol 37 (2) ◽  
pp. 199 ◽  
Author(s):  
G. Fathi ◽  
G. K. McDonald ◽  
R. C. M. Lance
Keyword(s):  
Grain Size ◽  
Grain Yield ◽  
Initial Response ◽  
Kernel Weight ◽  
High Yield ◽  
Malting Quality ◽  
Yield Response ◽  
Genotypic Differences ◽  
Barley Cultivars ◽  
N Rates

Summary. Genotypic differences in responses to nitrogen (N) fertiliser of 6 cultivars of barley (Clipper, Stirling, Weeah, Schooner, Chebec, Skiff) grown at 8 different rates of N were examined in 2 seasons. Measurements of vegetative growth, N content, grain yield, grain protein concentration (GPC) and yield components were taken to identify traits that may contribute to high yield responsiveness. The optimum rates of N for dry matter production at ear emergence (DMee) were greater than 80 kg N/ha for all cultivars and often growth increased up to 105 kg N/ha. Optimum rates of N for grain yield (Nopt) were lower and ranged, on average, from 50 kg N/ha for Clipper to 96 kg N/ha for Chebec. The initial response to N varied from 13–14 kg/kg N in Chebec, Weeah and Schooner, to 36 kg/kg N in Skiff. The Nopt for the semi-dwarf cultivar Skiff was 71 kg N/ha and it tended to show the greatest yield response to N. It produced 19 kernels/g DMee, compared with 15–17 kernels/g DMee in the other cultivars. Unlike most other cultivars, Skiff’s yield was consistently and positively correlated with ears/m2; Stirling was the only other cultivar to show a similar relationship. However, the average kernel weight of Skiff was up to 5 mg lower than that of Clipper, Weeah and Schooner, and varied more than these cultivars between sites, suggesting that consistent grain size may be a problem in this cultivar. By comparison, Clipper and Schooner had lower Nopt (51 kg/ha) and a less variable kernel weight. There were no signs of differences in GPC of the 6 cultivars used here at 3 N-responsive sites. Adding N increased GPC up to the highest rate of N and the responses were generally linear, but GPC at Nopt exceeded the upper limit for malting quality of 11.8% in all cultivars. Average N rates of between 38 kg N/ha (Schooner) and 58 kg N/ha (Skiff) were sufficient to raise GPC above 11.8%. The experiments showed that the N rates for optimum yields varied considerably among cultivars, but applyi1ng rates to achieve maximum yields may cause GPC to exceed the maximum value for malting barley. The use of semi-dwarf cultivars, such as Skiff, which are very responsive to N, can provide some leeway in the choice of N, but there may be a trade-off in quality associated with reduced grain size.

scholarly journals Structural variants and selective sweep foci contribute to insecticide resistance in the Drosophila melanogaster genetic reference panel

2018 ◽  
Author(s):  
Paul Battlay ◽  
Llewellyn Green ◽  
Pontus B. Leblanc ◽  
Joshua M. Schmidt ◽  
Alexandre Fournier-Level ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Selective Sweep ◽  
Association Studies ◽  
Transcript Abundance ◽  
Reference Panel ◽  
Drosophila Genome ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Number Variation

AbstractPatterns of nucleotide polymorphism within populations of Drosophila melanogaster suggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweep loci to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid). Genome wide association studies map ‘survival-on-malathion’ to two of the largest sweeps in the D. melanogaster genome; Ace and Cyp6g1. Malathion survivorship also correlates with lines which have high levels of Cyp12d1 and Jheh1 and Jheh2 transcript abundance. Permethrin phenotypes map to the largest cluster of P450 genes in the Drosophila genome, however in contrast to a selective sweep driven by insecticide use, the derived state seems to be associated with susceptibility. These results underscore previous findings that highlight the importance of structural variation to insecticide phenotypes: Cyp6g1 exhibits copy number variation and transposable element insertions, Cyp12d1 is tandemly duplicated, the Jheh loci are associated with a Bari1 transposable element insertion, and a Cyp6a17 deletion is associated with susceptibility.

scholarly journals Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112

2020 ◽  
Author(s):  
Yan Yang ◽  
Smit Dhakal ◽  
Chenggen Chu ◽  
Shichen Wang ◽  
Qingwu Xue ◽  
...  
Keyword(s):  
Grain Yield ◽  
Great Plains ◽  
Yield Components ◽  
Recombinant Inbred Lines ◽  
Wheat Breeding ◽  
Kernel Weight ◽  
Genetic Maps ◽  
Wheat Cultivars ◽  
Thousand Kernel Weight ◽  
Yield And Yield Components

AbstractTwo drought-tolerant wheat cultivars, ‘TAM 111’ and ‘TAM 112’, have been widely grown in the Southern Great Plains of the U.S. and used as parents in many wheat breeding programs worldwide. This study aimed to reveal genetic control of yield and yield components in the two cultivars under both dryland and irrigated conditions. A mapping population containing 124 F5:7 recombinant inbred lines (RILs) was developed from the cross of TAM 112/TAM 111. A set of 5,948 SNPs from the wheat 90K iSelect array and double digest restriction-site associated DNA sequencing was used to construct high-density genetic maps. Data for yield and yield components were obtained from 11 environments. QTL analyses were performed based on 11 individual environments, across all environments, within and across mega-environments. Thirty-six unique consistent QTL regions were distributed on 13 chromosomes including 1A, 1B, 1D, 2A, 2D, 3D, 4B, 4D, 6A, 6B, 6D, 7B, and 7D. Ten unique QTL with pleiotropic effects were identified on four chromosomes and eight were in common with the consistent QTL. These QTL increased dry biomass grain yield by 16.3 g m−2, plot yield by 28.1 g m−2, kernels spike−1 by 0.7, spikes m−2 by 14.8, thousand kernel weight by 0.9 g with favorable alleles from either parent. TAM 112 alleles mainly increased spikes m−2 and thousand kernel weight while TMA 111 alleles increased kernels spike−1, harvest index and grain yield. The saturated genetic map and markers linked to significant QTL from this study will be very useful in developing high throughput genotyping markers for tracking the desirable haplotypes of these important yield-related traits in popular parental cultivars.

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