Novel QTL Associated with Shoot Branching Identified in Doubled Haploid Rice (Oryza sativa L.) under Low Nitrogen Cultivation

Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica), grown under normal nitrogen and low nitrogen cultivation open field conditions. The results of the phenotypic evaluation indicated that parental lines 93-11 (P1, a high tillering indica cultivar) and Milyang352 (P2, a low tillering japonica cultivar) showed distinctive phenotypic responses, also reflected in their derived population. In addition, the linkage mapping and quantitative trait locus (QTL) analysis detected three QTLs associated with tiller number on chromosome 2 (qTNN2-1, 130 cM, logarithm of the odds (LOD) 4.14, PVE 14.5%; and qTNL2-1, 134 cM, LOD: 6.05, PVE: 20.5%) and chromosome 4 (qTN4-1, 134 cM, LOD 3.92, PVE 14.5%), with qTNL2-1 having the highest phenotypic variation explained, and the only QTL associated with tiller number under low nitrogen cultivation conditions, using Kompetitive Allele-Specific PCR (KASP) and Fluidigm markers. The additive effect (1.81) of qTNL2-1 indicates that the allele from 93-11 (P1) contributed to the observed phenotypic variation for tiller number under low nitrogen cultivation. The breakthrough is that the majority of the candidate genes harbored by the QTLs qTNL2-1 and qTNN4-1 (here associated with the control of shoot branching under low and normal nitrogen cultivation, respectively), were also proposed to be involved in plant stress signaling or response mechanisms, with regard to their annotations and previous reports. Therefore, put together, these results would suggest that a possible crosstalk exists between the control of plant growth and development and the stress response in rice.

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Identification of QTLs for dynamic and steady state photosynthetic traits in a barley mapping population

10.1101/2020.08.09.243352 ◽

2020 ◽

Author(s):

William T. Salter ◽

Si Li ◽

Peter M. Dracatos ◽

Margaret M. Barbour

Keyword(s):

Steady State ◽

Stomatal Conductance ◽

Doubled Haploid ◽

Mapping Population ◽

Yield Potential ◽

Doubled Haploid Population ◽

Photosynthetic Induction ◽

In Planta ◽

Activation Rate ◽

Rubisco Activation

AbstractEnhancing the photosynthetic induction response to fluctuating light has been suggested as a key target for improvement in crop breeding programs, with the potential to substantially increase whole canopy carbon assimilation and contribute to crop yield potential. Rubisco activation may be the main physiological process that will allow us to achieve such a goal. In this study, we phenotypically assessed the rubisco activation rate in a doubled haploid (DH) barley mapping population [131 lines from a Yerong/Franklin (Y/F) cross] after a switch from moderate to saturating light. Rates of rubisco activation were found to be highly variable across the mapping population, with a median activation rate of 0.1 min−1 in the slowest genotype and 0.74 min−1 in the fastest genotype. A QTL for rubisco activation rate was identified on chromosome 7H. This is the first report on the identification of a QTL for rubisco activation rate in planta and the discovery opens the door to marker assisted breeding to improve whole canopy photosynthesis of barley. Further strength is given to this finding as this QTL colocalised with QTLs identified for steady state photosynthesis and stomatal conductance. Several other distinct QTLs were identified for these steady state traits, with a common overlapping QTL on chromosome 2H, and distinct QTLs for photosynthesis and stomatal conductance identified on chromosomes 4H and 5H respectively. Future work should aim to validate these QTLs under field conditions so that they can be used to aid plant breeding efforts.HighlightSignificant variation exists in the photosynthetic induction response after a switch from moderate to saturating light across a barley doubled haploid population. A QTL for rubisco activation rate was identified on chromosome 7H, as well as overlapping QTLs for steady state photosynthesis and stomatal conductance.

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Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.)

Scientific Reports ◽

10.1038/s41598-020-59184-z ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 3

Author(s):

Mark Ian C. Calayugan ◽

Andrea Kariza Formantes ◽

Amery Amparado ◽

Gwen Iris Descalsota-Empleo ◽

Chau Thanh Nha ◽

...

Keyword(s):

Oryza Sativa ◽

Genetic Analysis ◽

Doubled Haploid ◽

Agronomic Traits ◽

Oryza Sativa L ◽

Doubled Haploid Population ◽

Iron And Zinc ◽

Zinc Concentrations ◽

Haploid Population

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Survei Polimorfisme Tetua untuk Pengembangan Panel CSSL Padi (Oryza sativa L.) dan Identifikasi Tanaman F1

Jurnal AgroBiogen ◽

10.21082/jbio.v10n3.2014.p85-92 ◽

2016 ◽

Vol 10 (3) ◽

pp. 85

Author(s):

Mariana Susilowati ◽

Panjisakti Basunanda ◽

Wening Enggraini ◽

Ma'sumah Ma'sumah ◽

Kurniawan R. Trijatmiko

Keyword(s):

Ssr Marker ◽

Oryza Sativa L ◽

Flag Leaf ◽

Polymorphic Marker ◽

Tiller Number ◽

Yield Potential ◽

Spikelet Number ◽

Donor Parent ◽

Segment Substitution ◽

Productive Tiller

Raising yield potential of modern indica varieties is essential to meet the increased demand of rice production. This is due to increased human population, threats of climate change and degradation of agricultural resources. The use of chromosome segment substitution lines (CSSL) is more effective for identification of genes those are useful for improvement of yield potential. The aims of this study were to observe the morphological trait differences between recipient parent (var. Ciherang) and three candidates of donor parent (var. Fatmawati and new plant type lines, i.e. B12743 and B11143D), to identify polymorphic SSR markers among them and to verify F1 individuals. Ciherang and B11143D showed significant differences on flowering time, plant height, flag leaf area, tiller number, productive tiller number, panicle length, spikelet number per panicle and 1,000 grain weight. The rate of SSR marker polymorphisms between Ciherang and B11143D was the highest, where 155 of 513 markers (30.2%) were polymorphic. Marker genotyping using three polymorphic markers showed that 26 of 27 plants resulted from the cross of Ciherang х B11143D were F1. These F1 plants could become the basis of CSSL panel that facilitate the mapping of genes responsible for increasing the yield potential.

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QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Genes ◽

10.3390/genes12040604 ◽

2021 ◽

Vol 12 (4) ◽

pp. 604

Author(s):

Paolo Vitale ◽

Fabio Fania ◽

Salvatore Esposito ◽

Ivano Pecorella ◽

Nicola Pecchioni ◽

...

Keyword(s):

Candidate Genes ◽

Recombinant Inbred Lines ◽

Snp Array ◽

Heading Date ◽

Tiller Number ◽

Genetic Maps ◽

Yield Potential ◽

Adaptation To Climate Change ◽

Map Resolution ◽

Mapping Populations

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

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Mapping QTL for spike fertility and related traits in two doubled haploid wheat (Triticum aestivum L.) populations

BMC Plant Biology ◽

10.1186/s12870-021-03061-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nicole Pretini ◽

Leonardo S. Vanzetti ◽

Ignacio I. Terrile ◽

Guillermo Donaire ◽

Fernanda G. González

Keyword(s):

Doubled Haploid ◽

Marker Assisted Selection ◽

Triticum Aestivum L ◽

Physiological Model ◽

Yield Potential ◽

Breeding Programs ◽

Per Se ◽

Genomic Regions ◽

Fertility Traits ◽

Selection Of

Abstract Background In breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with higher grains per spike (GN) and occasionally increased grain weight (GW) (main numerical components of the yield). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two doubled haploid (DH) populations (Baguette Premium 11 × BioINTA 2002 and Baguette 19 × BioINTA 2002). Results In total 305 QTL were identified for 14 traits, out of which 12 QTL were identified in more than three environments and explained more than 10% of the phenotypic variation in at least one environment. Eight hotspot regions were detected on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B in which at least two major and stable QTL sheared confidence intervals. QTL on two of these regions (R5A.1 and R5A.2) have previously been described, but the other six regions are novel. Conclusions Based on the pleiotropic analysis within a robust physiological model we conclude that two hotspot genomic regions (R5A.1 and R5A.2) together with the QGW.perg-6B are of high relevance to be used in marker assisted selection in order to improve the spike yield potential. All the QTL identified for the spike related traits are the first step to search for their candidate genes, which will allow their better manipulation in the future.

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Morphological and physiological plasticity response to low nitrogen stress in black cottonwood (Populus deltoides Marsh.)

Journal of Forestry Research ◽

10.1007/s11676-021-01338-4 ◽

2021 ◽

Author(s):

Cun Chen ◽

Yanguang Chu ◽

Qinjun Huang ◽

Changjun Ding ◽

Weixi Zhang ◽

...

Keyword(s):

Negative Correlation ◽

Nitrogen Use Efficiency ◽

Root Biomass ◽

Populus Deltoides ◽

Leaf Traits ◽

Nitrogen Level ◽

Nitrogen Use ◽

Use Efficiency ◽

Normal Nitrogen ◽

Low Nitrogen

AbstractIt is important to evaluate nitrogen use efficiency and nitrogen tolerance of trees in order to improve their productivity. In this study, both were evaluated for 338 Populus deltoides genotypes from six provenances. The plants were cultured under normal nitrogen (750 μM NH4NO3) and low nitrogen (5 μM NH4NO3) conditions for 3 months. Growth, chlorophyll content and glutamine synthetase activity of each genotype were measured. Under low nitrogen, heights, ground diameter, leaf area, leaf and root biomass, and chlorophyll contents were significantly lower than those under normal nitrogen level. Correlation analysis showed that nutrient distribution changed under different nitrogen treatments. There was a negative correlation between leaf traits and root biomass under normal nitrogen level, however, the correlation became positive in low nitrogen treatment. Moreover, with the decrease of nitrogen level, the negative correlation between leaf morphology and chlorophyll levels became weakened. The growth of the genotypes under the two treatments was evaluated by combining principal component analysis with a fuzzy mathematical membership function; the results showed that leaf traits accounted for a large proportion of the variation in the evaluation model. According to the results of comprehensive evaluation of plants under the two treatments, the 338 P. deltoides genotypes could be divided into nine categories, with wide genotypic diversity in nitrogen use efficiency and low nitrogen tolerance. As a result, 26 N-efficient genotypes and 24 N-inefficient genotypes were selected. By comparative analysis of their morphological and physiological traits under the two treatments, leaf traits could be significant indicators for nitrogen use efficiency and nitrogen tolerance, which is of considerable significance for breeding poplar varieties with high nitrogen use efficiencies.

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Direct PCR-based genetic mapping of rice telomeric repeat associated sequences

Genome ◽

10.1139/g98-002 ◽

1998 ◽

Vol 41 (2) ◽

pp. 193-198 ◽

Cited By ~ 5

Author(s):

Lishuang Shen ◽

Lihuang Zhu

Keyword(s):

Genetic Mapping ◽

Oryza Sativa L ◽

Telomeric Repeat ◽

Doubled Haploid Population ◽

Direct Pcr ◽

Japonica Variety ◽

Rapd Primer ◽

Associated Sequences ◽

Haploid Population ◽

Pcr Method

Direct PCR-based genetic mapping of telomeric repeat associated sequences (TASs) was achieved using a RAPD primer mediated asymmetric PCR method. Twenty-two TAS loci were mapped in a rice doubled haploid population derived from a cross between an indica variety (Zhaiyeqing8) and a japonica variety (Jingxi17). Of these, 11 loci were mapped to the most distal position of seven chromosome arms and lengthened the linkage groups by 7.4-22.6 cM, five were mapped to the approximate positions of the centromeric regions, and six were mapped to other interstitial chromosomal regions.Key words: rice, Oryza sativa L., genetic mapping, telomeric repeat, telomeric repeat associated sequences, RAPD primer mediated PCR.

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