Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

Abstract Background Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Results Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. Conclusions The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

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Characterization of quantitative trait locus for days to heading in near-isogenic lines with genetic background of Indica-type rice variety IR64 (Oryza sativa)

Plant Breeding ◽

10.1111/j.1439-0523.2011.01864.x ◽

2011 ◽

Vol 130 (5) ◽

pp. 526-532 ◽

Cited By ~ 9

Author(s):

Daisuke Fujita ◽

Rizza E. Santos ◽

Leodegario A. Ebron ◽

Yoshimichi Fukuta ◽

Nobuya Kobayashi

Keyword(s):

Quantitative Trait Locus ◽

Oryza Sativa ◽

Quantitative Trait ◽

Genetic Background ◽

Rice Variety ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Days To Heading ◽

Trait Locus

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Fine mapping of a grain weight quantitative trait locus, qGW6, using near isogenic lines derived from Oryza rufipogon IRGC105491 and Oryza sativa cultivar MR219

Genetics and Molecular Research ◽

10.4238/2014.november.11.13 ◽

2014 ◽

Vol 13 (4) ◽

pp. 9477-9488 ◽

Cited By ~ 3

Author(s):

M.S. Ngu ◽

M.J. Thomson ◽

M.A.R. Bhuiyan ◽

C. Ho ◽

R. Wickneswari

Keyword(s):

Quantitative Trait Locus ◽

Oryza Sativa ◽

Fine Mapping ◽

Quantitative Trait ◽

Oryza Rufipogon ◽

Grain Weight ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Trait Locus

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Verification of quantitative trait locus for stickiness of cooked rice and amylose content by developing near-isogenic lines

Breeding Science ◽

10.1270/jsbbs.58.235 ◽

2008 ◽

Vol 58 (3) ◽

pp. 235-242 ◽

Cited By ~ 14

Author(s):

Asako Kobayashi ◽

Katsura Tomita ◽

Faming Yu ◽

Yoshinobu Takeuchi ◽

Masahiro Yano

Keyword(s):

Quantitative Trait Locus ◽

Quantitative Trait ◽

Amylose Content ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Cooked Rice ◽

Trait Locus

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Development of near-isogenic lines targeting a major QTL on 3AL for pre-harvest sprouting resistance in bread wheat

Crop and Pasture Science ◽

10.1071/cp17423 ◽

2018 ◽

Vol 69 (9) ◽

pp. 864 ◽

Cited By ~ 5

Author(s):

Xingyi Wang ◽

Hui Liu ◽

Md Sultan Mia ◽

Kadambot H. M. Siddique ◽

Guijun Yan

Keyword(s):

Quantitative Trait ◽

Wheat Chromosome ◽

Triticum Aestivum L ◽

Phenotypic Trait ◽

Resistance Locus ◽

Near Isogenic Lines ◽

Resistant Parent ◽

Functional Studies ◽

Isogenic Lines ◽

Trait Locus

Resistance to pre-harvest sprouting (PHS) in wheat (Triticum aestivum L.) is one of the most valuable traits in many breeding programs. However, the quantitative nature of inheritance of PHS resistance challenges the study of this trait. Near-isogenic lines (NILs) can turn a complicated quantitative trait into a Mendelian factor (qualitative) and are, therefore, valuable materials for identification of the gene(s) responsible for a specific phenotypic trait and for functional studies of specific loci. Five pairs of NILs were developed and confirmed for a major quantitative trait locus (QTL) located on the long arm of chromosome 3A contributing to PHS resistance in wheat. These NILs were generated by using the heterogeneous inbred family method and a fast generation-cycling system. Significant differences in PHS resistance between the isolines were detected in the NILs. The presence of the PHS-resistance allele from the resistant parent increased resistance to sprouting on spikes by 26.7–96.8%, with an average of 73.8%, and increased seed dormancy by 36.9–87.2%, with an average of 59.9% across the NILs. These NILs are being used for the identification of candidate genes responsible for this major PHS-resistance locus on wheat chromosome arm 3AL.

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Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon

Plants ◽

10.3390/plants11010008 ◽

2021 ◽

Vol 11 (1) ◽

pp. 8

Author(s):

Siyoung Lee ◽

Girim Park ◽

Yunseo Choi ◽

Seoyeon Park ◽

Hoytaek Kim ◽

...

Keyword(s):

Genomic Region ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Near Isogenic Lines ◽

Genome Resequencing ◽

Isogenic Lines ◽

Genome Wide ◽

Donor Parent ◽

Caps Markers ◽

Whole Genome Resequencing

Trans-lycopene is a functional phytochemical abundant in red-fleshed watermelons, and its contents vary among cultivars. In this study, the genetic basis of high trans-lycopene contents in scarlet red flesh was evaluated. Three near-isogenic lines (NILs) with high trans-lycopene contents were derived from the scarlet red-fleshed donor parent DRD and three coral red-fleshed (low trans-lycopene contents) recurrent parents. The lycopene contents of DRD (589.4 ± 71.8 µg/g) were two times higher than that of the recurrent parents, and values for NILs were intermediate between those of the parents. Coral red-fleshed lines and F1 cultivars showed low trans-lycopene contents (135.7 ± 18.0 µg/g to 213.7 ± 39.5 µg/g). Whole-genome resequencing of two NILs and their parents and an analysis of genome-wide single-nucleotide polymorphisms revealed three common introgressed regions (CIRs) on chromosomes 6, 9, and 10. Twenty-eight gene-based cleaved amplified polymorphic sequence (CAPS) markers were developed from the CIRs. The CAPS markers derived from CIR6 on chromosome 6, spanning approximately 1 Mb, were associated (R2 = 0.45–0.72) with the trans-lycopene contents, particularly CIR6-M1 and CIR6-M4. Our results imply that CIR6 is a major genomic region associated with variation in the trans-lycopene contents in red-fleshed watermelon, and CIR6-M1 and CIR6-M4 may be useful for marker-assisted selection.

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