Dissection of the genetic architecture for tassel branch number by QTL analysis in two related populations in maize

Full-sib and selfed (S1) progenies were obtained from sub-populations of ESALQ-PB1, divergently selected for tassel size (T+ and T-) and ear height (E+ and E-), and used for estimating genetic and phenotypic correlation coefficients between traits. The analyzed traits were: EW- total ear weight (g/plant), PH- plant height (cm), EH- ear height (cm), TB- tassel branch number and TL- tassel length. The highest genetic (rG) and phenotypic (rF) correlation was observed for the combination PH x EH, as expected, with average of 0.800 and 0.778, respectively over sub-populations and locations. It is apparent that divergent selection for tassel size did not affect greatly the correlation between PH and EH in the full sib progenies, but in the inbred progenies the correlation was smaller in the sub-population selected for larger tassels. Genetic correlation between PH and EH with tassel traits was always positive but ranged from 0.020 to 0.668 in Piracicaba and from 0.06 to 0.309 in Rio Verde. Genetic correlation between PH and EH with yield (EW) also was positive in the range of 0.087 to 0.503. EH showed higher correlation with EW in relation to PH x EW and differences were larger in the sub-populations divergently selected for ear height. Correlation between tassel traits with other traits was positive in most of instances and a lack of consistency was observed among sub-populations. Generally the coefficients of genetic and phenotypic correlation differed substantially from the estimates in the base population ESALQ-PB1 before divergent selection for tassel size and ear placement. Divergent selection affected the correlation between traits under unpredicted and varying magnitudes.

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Combined GWAS and QTL analysis for dissecting the genetic architecture of kernel test weight in maize

Molecular Genetics and Genomics ◽

10.1007/s00438-019-01631-2 ◽

2019 ◽

Vol 295 (2) ◽

pp. 409-420 ◽

Cited By ~ 4

Author(s):

Xiaoxiang Zhang ◽

Zhongrong Guan ◽

Lei Wang ◽

Jun Fu ◽

Yinchao Zhang ◽

...

Keyword(s):

Qtl Analysis ◽

Genetic Architecture ◽

Test Weight

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QTL Mapping and integration as well as candidate gene prediction for branch number in soybean

10.1101/2019.12.27.889287 ◽

2019 ◽

Author(s):

Yuhua Yang ◽

Yang Lei ◽

Zhiyuan Bai ◽

Yichao Wei ◽

Ruijun Zhang

Keyword(s):

Genetic Architecture ◽

Genetic Basis ◽

Interaction Analysis ◽

Gene Prediction ◽

Phenotypic Variance ◽

Environment Interaction ◽

Orthologous Genes ◽

Branch Number ◽

Lateral Organs ◽

Major Qtl

AbstractBranch number is an important factor that affects crop plant architecture and yield in soybean. With the aim of elucidating the genetic basis of branch number, we identified 10 consensus quantitative trait loci (QTLs) through preliminary mapping, which were on chromosome A1, B2, C1, C2, D1a, D1b, F, L and N, explained 0.3-33.3% of the phenotypic variance. Of these, three QTLs were identical to previously identified ones, whereas the other seven were novel. In addition, one major QTL-qBN.C2 (R2=33.3%) was detected in all three environments and another new major QTL-qBN.N (R2=19.6%) was detected in two environments (Taiyuan 2017 and Taiyuan 2018), but only in Taiyuan. Thus, the QTL × environment interaction analysis confirmed that QTL-qBN.N was strongly affected by the environment. We compared the physical positions of the QTL intervals of the candidate genes potentially involved in branching development, and five orthologous genes were ultimately selected and related to the establishment of axillae meristem organization and lateral organs, qBN.A1 (SoyZH13_05G177000.m1), qBN.C2 (SoyZH13_06G176500.m1, SoyZH13_06G185600.m1), and qBN.D1b-1 (SoyZH13_02G035400.m1, SoyZH13_02G070000.m3). The results of our study reveal a complex and relatively complete genetic architecture and can serve as a basis for the positional gene cloning of branch number in soybean.

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Potential of twenty exotic germplasms to improve Brazilian maize architecture

Brazilian Journal of Genetics ◽

10.1590/s0100-84551997000400022 ◽

1997 ◽

Vol 20 (4) ◽

pp. 691-969 ◽

Cited By ~ 5

Author(s):

Amadeu Regitano Neto ◽

Luciano Lourenço Nass ◽

José Branco de Miranda Filho

Keyword(s):

Block Design ◽

Correlation Coefficients ◽

Phenotypic Correlation ◽

Maize Breeding ◽

Branch Number ◽

Population Means ◽

Local Populations ◽

Randomized Complete Block Design ◽

Tassel Branch Number ◽

Ear Height

Temperate and temperate x tropical germplasms were introduced into the maize breeding of the Department of Genetics (ESALQ-USP). Twenty populations designated as P-1 to P-20 and a check population were evaluated in a randomized complete block design with two replications at Piracicaba, SP, Brazil. Plots were 2.0 m long, spaced 1.0 m apart, with 10 plants per plot after thinning. The following traits were evaluated: PH, plant height; EH, ear height; TB, tassel branch number; KW, 100 kernels weight; EL, ear length; ED, ear diameter; KR, kernels per row, and RN, number of rows of kernels. The means of the exotic populations showed a variation in performance for all traits. The population means were greater than check means for KW, EL, and KR. Populations P-9, P-10, P-12, and P-13 showed low relative ear placement values (EH/PH index), indicating that these materials could contribute to lower ear placement in local populations. P-1 and P-9 showed a high potential to reduce TB. The phenotypic correlation coefficients among populations were positive for most combinations, except for RN with PH, EH, TB, and KW. Predictions of 19 composite means were obtained for all traits.

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Genetic Architecture of Chile Pepper (Capsicum Spp.) QTLome Revealed Using Meta-QTL Analysis

10.21203/rs.3.rs-153361/v1 ◽

2021 ◽

Author(s):

Dennis N. Lozada ◽

Lanie Whelpley ◽

Andrea Acuña-Galindo

Keyword(s):

Qtl Analysis ◽

Genetic Architecture ◽

Meta Analysis ◽

Phytophthora Capsici ◽

Snp Markers ◽

Vegetable Crops ◽

Chile Pepper ◽

Breeding Populations ◽

Capsicum Spp ◽

Chile Peppers

Abstract Chile peppers (Capsicum spp.) are among the most important vegetable crops in the world due to their health-related, economic, and industrial uses. In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS) in peppers. Meta-QTL analysis for different traits in Capsicum remains lacking, and therefore it would be necessary to re-evaluate identified QTL for a more precise MAS for genetic improvement. We report the first known meta-QTL analysis for diverse traits in the chile pepper QTLome. A literature survey using 29 published linkage mapping studies identified 766 individual QTL from five different trait classes. A total of 311 QTL were projected into a consensus map. Meta-analysis identified 30 meta-QTL regions distributed across the 12 chromosomes of Capsicum. MQTL5.1 and MQTL5.2 related to Phytophthora capsici fruit and root rot resistance were delimited to < 1.0 cM confidence intervals in chromosome P5. Candidate gene analysis for the flanking sequences for the P5 meta-QTL revealed biological functions related to DNA repair and transcription regulation. Moreover, epigenetic mechanisms such as histone and RNA methylation and demethylation were predicted, indicating the potential role of epigenetics for P. capsici resistance. Allele specific SNP markers for the meta-QTL will be developed and validated using different breeding populations of Capsicum for MAS of P. capsici resistant lines. Altogether, results from meta-QTL analysis for chile pepper QTLome rendered further insights into the genetic architecture of different traits for this valuable horticultural crop.

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