Screening for a Novel Gene, OsPSLSq6, Using QTL Analysis for Lodging Resistance in Rice

Lodging is the most common factor that affects crop productivity, reducing yield, grain quality, and harvesting efficiency of rice and other cereal crops. The Cheongcheong (Indica)/Nagdong (Japonica) doubled haploid (CNDH) genetic map was used to develop a lodging-resistant variety. The major agricultural traits of rice related to lodging resistance, such as the pushing strength of the lower stem before the heading date (PSLSB) at reproductive growth period and pushing strength of the lower stem after the heading date (PSLSA) at full ripe period were investigated. A quantitative trait locus (QTL) analysis of PSLSA and PSLSB detected on RM439-RM20318 on chromosome 6 has overlap in three consecutive years. RM439-RM20318 on chromosome 6 contained 15 lodging resistance candidate genes. Among the candidate genes, Os06g0623200, named OsPSLSq6, which is similar to Cinnamoyl-CoA reductase, involved lignin biosynthesis in defense responses. Lignin is the main structural component of vascular plants’ secondary cell wall, which is not only related to plant growth and development but also to mechanical strength. OsPSLSq6 opens new possibilities to control lignin synthesis to improve lodging resistance. OsPSLSq6 can be used as a target gene for further studies to provide important information for the marker-assisted improvement of target traits and cloning genes underlying the QTL of interest.

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Identification of Candidate Gene for Internode Length in Rice to Enhance Resistance to Lodging Using QTL Analysis

Plants ◽

10.3390/plants10071369 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1369

Author(s):

Dan-Dan Zhao ◽

Ju-Hyeong Son ◽

Muhammad Farooq ◽

Kyung-Min Kim

Keyword(s):

Candidate Genes ◽

Qtl Analysis ◽

Middle Part ◽

Internode Length ◽

Stem Diameter ◽

Chromosome 1 ◽

Doubled Haploid Population ◽

Lodging Resistance ◽

Cytochrome P450 Family ◽

Uppermost Internode

Internode length and stem diameter are the primary traits affecting the lodging resistance of rice. Traits related to the length of the panicle (LP), uppermost internode (LUI), second internode (LSI), third internode (LTI), fourth internode (LFI), lowest internode (LLI) as well as stem diameter at the uppermost internode (SDUI), second internode (SDSI), third internode (SDTI), fourth internode (SDFI), and lowest internode (SDLI) in 120 Cheongcheong/Nagdong doubled haploid population were investigated using a quantitative trait locus (QTL) analysis. Thirty-four QTL regions affected LP and the length of each internode. Twenty-six QTL regions were associated with the stem diameter of each internode. RM12285-RM212 on chromosome 1 contained 10 QTLs related to the internode length, which have overlapped for over 2 years. Twenty-three candidate genes were screened using mark interval. Among the candidate genes, Os01g0803900, named OsCYPq1, which is in the Cytochrome P450 family, might be involved in gibberellins (GA) synthesis. GA is an essential plant growth regulator that affects plant height. OsCYPq1 catalyzes oxidation steps in the middle part of the GA pathway. OsCYPq1 is expected to provide valuable information to improve the marker assessment for target traits and QTL gene cloning in rice.

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QTL Analysis for Plant Height and Heading Date in Rice under Two Nitrogen Levels

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2011.01525 ◽

2011 ◽

Vol 37 (9) ◽

pp. 1525-1532 ◽

Cited By ~ 1

Author(s):

Yue FENG ◽

Rong-Rong ZHAI ◽

Li-Yong CAO ◽

Ze-Chuan LIN ◽

Xing-Hua WEI ◽

...

Keyword(s):

Plant Height ◽

Qtl Analysis ◽

Heading Date ◽

Nitrogen Levels

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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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Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

Scientific Reports ◽

10.1038/s41598-021-91446-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jose Miguel Soriano ◽

Pasqualina Colasuonno ◽

Ilaria Marcotuli ◽

Agata Gadaleta

Keyword(s):

Molecular Markers ◽

Abiotic Stress ◽

Durum Wheat ◽

Candidate Genes ◽

Biotic Stress ◽

Qtl Analysis ◽

Complex Traits ◽

Genetic Basis ◽

Agronomic Traits ◽

Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

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Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽

10.3390/genes12050718 ◽

2021 ◽

Vol 12 (5) ◽

pp. 718

Author(s):

Bingxin Meng ◽

Tao Wang ◽

Yi Luo ◽

Deze Xu ◽

Lanzhi Li ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Association Analysis ◽

Genome Wide Association Study ◽

Flag Leaf ◽

Genome Wide Association ◽

Lodging Resistance ◽

Leaf Type ◽

Stem Strength ◽

Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

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QTL analysis for heading date using recombinant inbred lines in rice

Rice Genetics Collection - Rice Genetics II ◽

10.1142/9789812814319_0091 ◽

2008 ◽

pp. 240-243

Author(s):

M. Oda ◽

H. Yasui ◽

A. Yoshimura

Keyword(s):

Qtl Analysis ◽

Recombinant Inbred ◽

Recombinant Inbred Lines ◽

Heading Date ◽

Inbred Lines

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Hop Polyphenols in Relation to Verticillium Wilt Resistance and Their Antifungal Activity

Plants ◽

10.3390/plants9101318 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1318

Author(s):

Sabina Berne ◽

Nataša Kovačević ◽

Damijana Kastelec ◽

Branka Javornik ◽

Sebastjan Radišek

Keyword(s):

Phenolic Compounds ◽

Antifungal Activity ◽

Verticillium Wilt ◽

Molecular Mechanisms ◽

Induced Defense ◽

Fungal Growth ◽

Defense Responses ◽

Resistant Variety ◽

Phenological Stages ◽

Total Polyphenols

(1) Background: Verticillium wilt (VW) of hop is a devastating disease caused by the soil-borne fungi Verticillium nonalfalfae and Verticillium dahliae. As suggested by quantitative trait locus (QTL) mapping and RNA-Seq analyses, the underlying molecular mechanisms of resistance in hop are complex, consisting of preformed and induced defense responses, including the synthesis of various phenolic compounds. (2) Methods: We determined the total polyphenolic content at two phenological stages in roots and stems of 14 hop varieties differing in VW resistance, examined the changes in the total polyphenols of VW resistant variety Wye Target (WT) and susceptible Celeia (CE) on infection with V. nonalfalfae, and assessed the antifungal activity of six commercial phenolic compounds and total polyphenolic extracts from roots and stems of VW resistant WT and susceptible CE on the growth of two different V. nonalfalfae hop pathotypes. (3) Results: Generally, total polyphenols were higher in roots than stems and increased with maturation of the hop. Before flowering, the majority of VW resistant varieties had a significantly higher content of total polyphenols in stems than susceptible varieties. At the symptomatic stage of VW disease, total polyphenols decreased in VW resistant WT and susceptible CE plants in both roots and stems. The antifungal activity of total polyphenolic extracts against V. nonalfalfae was higher in hop extracts from stems than those from roots. Among the tested phenolic compounds, only p-coumaric acid and tyrosol markedly restricted fungal growth. (4) Conclusions: Although the correlation between VW resistance and total polyphenols content is not straightforward, higher levels of total polyphenols in the stems of the majority of VW resistant hop varieties at early phenological stages probably contribute to fast and efficient activation of signaling pathways, leading to successful defense against V. nonalfalfae infection.

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Effects of Multiple Planting Densities on Lignin Metabolism and Lodging Resistance of the Strip Intercropped Soybean Stem

Agronomy ◽

10.3390/agronomy10081177 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1177 ◽

Cited By ~ 1

Author(s):

Bin Cheng ◽

Ali Raza ◽

Li Wang ◽

Mei Xu ◽

Junji Lu ◽

...

Keyword(s):

Resistance Index ◽

Lignin Biosynthesis ◽

Planting Density ◽

Growth Stages ◽

Regulation Mechanism ◽

Key Factors ◽

Lodging Resistance ◽

Factors Affecting ◽

System A ◽

Lignin Metabolism

The shading of maize and self-shading are the key factors affecting the stem lignin biosynthesis and lodging resistance of soybean at middle and later growth stages in the strip intercropping system. A study was designed to explore the regulation mechanism of lignin metabolism and different planting densities; PD1, PD2, and PD3 were used having a total number of 17 plants m−2, 20 plants m−2, and 25 plants m−2, respectively, on the lodging resistance of strip intercropped soybean stem. Our results depicted that the lower planting density (PD1) appropriately promoted the leaf photosynthesis activities (Pn), increase the activity of lignin-related enzymes and the accumulation of carbohydrates in stems, and eventually enhanced the lodging resistance of the strip intercropped soybean stem. Correlation analysis also showed that the lodging resistance index of soybean stem was significantly correlated with the available light for soybean canopy and Pn strip intercropped soybean stem characteristics and activities of enzymes related to lignin synthesis among the different planting densities. The findings of our research will be useful in future studies to understand the relationship between different light environment, planting densities, and lodging resistance of intercropped soybean and also guide the optimum planting density in maize–soybean intercropping system.

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