Near-isogenic lines developed for a major QTL on chromosome arm 4HL conferring Fusarium crown rot resistance in barley

AbstractBackgroundFusarium crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. One of the putative quantitative trait locus (QTL) designated as Qcrs.cpi-1H has been previously mapped on chromosome arm 1HL in barley.ResultsIn this study, five pairs of near-isogenic lines (NILs) targeting the 1HL locus were developed. Analysing the NILs found that the resistant allele at Qcrs.cpi-1H significantly reduced FCR severity. Transcriptomic analysis was then conducted against three of the NIL pairs, which placed the Qcrs.cpi-1H locus in an interval spanning about 11 Mbp. A total of 56 expressed genes bearing SNPs were detected in this interval, which would facilitate detailed mapping as well as cloning gene(s) underlying the resistance locus. Also, five differentially expressed genes (DEGs) bearing non-synonymous SNPs were identified in the interval. Differences in DEGs regulated by Qcrs.cpi-1H those by Qcrs.cpi-4H (another known locus conferring FCR resistance) indicate that different mechanisms could be involved in their resistance.ConclusionNILs developed in this study and the transcriptomic sequences obtained from them did not only allow the validation of the resistance locus Qcrs.cpi-1H and the identification of candidate genes underlying its resistance, they also allowed the delineation of the resistance locus and the development of SNPs markers which formed a solid base for detailed mapping as well as cloning gene(s) underlying the locus.

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Delineating a locus conferring Fusarium crown rot resistance on chromosome arm 1HL in barley by developing and analysing a large population derived from near isogenic lines

The Crop Journal ◽

10.1016/j.cj.2020.03.008 ◽

2020 ◽

Vol 8 (6) ◽

pp. 1002-1010

Author(s):

Shang Gao ◽

Zhi Zheng ◽

Haiyan Hu ◽

Yunfeng Jiang ◽

Miao Liu ◽

...

Keyword(s):

Large Population ◽

Crown Rot ◽

Near Isogenic Lines ◽

Fusarium Crown Rot ◽

Isogenic Lines ◽

Chromosome Arm

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Validation and delineation of a locus conferring Fusarium crown rot resistance on 1HL in barley by analysing transcriptomes from multiple pairs of near isogenic lines

BMC Genomics ◽

10.1186/s12864-019-6011-8 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 3

Author(s):

Shang Gao ◽

Zhi Zheng ◽

Jonathan Powell ◽

Ahsan Habib ◽

Jiri Stiller ◽

...

Keyword(s):

Crown Rot ◽

Near Isogenic Lines ◽

Fusarium Crown Rot ◽

Isogenic Lines

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Detection of a major QTL conditioning trichome length and density on chromosome arm 4BL and development of near isogenic lines targeting this locus in bread wheat

Molecular Breeding ◽

10.1007/s11032-021-01201-8 ◽

2021 ◽

Vol 41 (2) ◽

Author(s):

Zhitong Chen ◽

Zhi Zheng ◽

Wei Luo ◽

Hong Zhou ◽

Zhaoyang Ying ◽

...

Keyword(s):

Bread Wheat ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Chromosome Arm ◽

Major Qtl

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Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.)

Theoretical and Applied Genetics ◽

10.1007/s00122-019-03359-4 ◽

2019 ◽

Vol 132 (8) ◽

pp. 2367-2379 ◽

Cited By ~ 8

Author(s):

Panfeng Guan ◽

Na Di ◽

Qing Mu ◽

Xueyi Shen ◽

Yongfa Wang ◽

...

Keyword(s):

Triticum Aestivum ◽

Bread Wheat ◽

Triticum Aestivum L ◽

Grain Weight ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Major Qtl

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Mapping and validation of a major QTL for primary root length of soybean seedlings grown in hydroponic conditions

BMC Genomics ◽

10.1186/s12864-021-07445-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Huatao Chen ◽

Giriraj Kumawat ◽

Yongliang Yan ◽

Baojie Fan ◽

Donghe Xu

Keyword(s):

Qtl Analysis ◽

Phenotypic Variation ◽

Root Length ◽

Primary Root ◽

Near Isogenic Lines ◽

Isogenic Lines ◽

Ril Population ◽

Hydroponic Conditions ◽

Primary Root Length ◽

Major Qtl

Abstract Background The root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative trait loci (QTL) associated with primary root length (PRL) during soybean seedling growth in hydroponic conditions. A total of 103 F7 recombinant inbred lines (RILs) derived from a cross between K099 (short primary root) and Fendou 16 (long primary root) were used to identify QTL for PRL in soybean. The RIL population was genotyped with 223 simple sequence repeats markers covering 20 chromosomes. Phenotyping for primary root length was performed for 3-weeks plants grown in hydoponic conditions. The identified QTL was validated in near isogenic lines and in a separate RIL population. Results QTL analysis using inclusive composite interval mapping method identified a major QTL on Gm16 between SSR markers Sat_165 and Satt621, explaining 30.25 % of the total phenotypic variation. The identified QTL, qRL16.1, was further confirmed in a segregating population derived from a residual heterozygous line (RHLs-98). To validate qRL16.1 in a different genetic background, QTL analysis was performed in another F6 RIL population derived from a cross between Union (medium primary root) and Fendou 16, in which a major QTL was detected again in the same genomic region as qRL16.1, explaining 14 % of the total phenotypic variation for PRL. In addition, the effect of qRL16.1 was confirmed using two pair of near-isogenic lines (NILs). PRL was significantly higher in NILs possessing the qRL16.1 allele from Fendou 16 compared to allele from K099. Conclusions The qRL16.1 is a novel QTL for primary root length in soybean which provides important information on the genetic control of root development. Identification of this major QTL will facilitate positional cloning and DNA marker-assisted selection for root traits in soybean.

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Plant Height Affects Fusarium Crown Rot Severity in Wheat

Phytopathology ◽

10.1094/phyto-05-10-0142 ◽

2010 ◽

Vol 100 (12) ◽

pp. 1276-1281 ◽

Cited By ~ 27

Author(s):

Y. X. Liu ◽

X. M. Yang ◽

J. Ma ◽

Y. M. Wei ◽

Y. L. Zheng ◽

...

Keyword(s):

Plant Height ◽

Crown Rot ◽

Near Isogenic Lines ◽

Height Difference ◽

Fusarium Crown Rot ◽

Defense Gene ◽

Reduced Height ◽

Rht Genes ◽

Per Se ◽

The Difference

Effects of plant height on Fusarium crown rot (FCR) disease severity were investigated using 12 pairs of near-isogenic lines (NILs) for six different reduced height (Rht) genes in wheat. The dwarf isolines all gave better FCR resistance when compared with their respective tall counterparts, although the Rht genes involved in these NILs are located on several different chromosomes. Treating plants with exogenous gibberellin increased FCR severity as well as seedling lengths in all of the isolines tested. Analysis of the expression of several defense genes with known correlation with resistance to FCR pathogens between the Rht isolines following FCR inoculation indicated that the better resistance of the dwarf isolines was not due to enhanced defense gene induction. These results suggested that the difference in FCR severity between the tall and dwarf isolines is likely due to their height difference per se or to some physiological and structural consequences of reduced height. Thus, caution should be taken when considering to exploit any FCR locus located near a height gene.

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