Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation

Abstract Leaf rolling is an important mechanism to mitigate the effects of moisture stress in several plant species. In the present study, a set of 92 wheat recombinant inbred lines derived from the cross between NI5439 × HD2012 were used to identify QTLs associated with leaf rolling under moisture stress condition. Linkage map was constructed using Axiom 35 K Breeder’s SNP Array and microsatellite (SSR) markers. A linkage map with 3661 markers comprising 3589 SNP and 72 SSR markers spanning 22,275.01 cM in length across 21 wheat chromosomes was constructed. QTL analysis for leaf rolling trait under moisture stress condition revealed 12 QTLs on chromosomes 1B, 2A, 2B, 2D, 3A, 4A, 4B, 5D, and 6B. A stable QTL Qlr.nhv-5D.2 was identified on 5D chromosome flanked by SNP marker interval AX-94892575–AX-95124447 (5D:338665301–5D:410952987). Genetic and physical map integration in the confidence intervals of Qlr.nhv-5D.2 revealed 14 putative candidate genes for drought tolerance which was narrowed down to six genes based on in-silico analysis. Comparative study of leaf rolling genes in rice viz., NRL1, OsZHD1, Roc5, and OsHB3 on wheat genome revealed five genes on chromosome 5D. Out of the identified genes, TraesCS5D02G253100 falls exactly in the QTL Qlr.nhv-5D.2 interval and showed 96.9% identity with OsZHD1. Two genes similar to OsHB3 viz. TraesCS5D02G052300 and TraesCS5D02G385300 exhibiting 85.6% and 91.8% identity; one gene TraesCS5D02G320600 having 83.9% identity with Roc5 gene; and one gene TraesCS5D02G102600 showing 100% identity with NRL1 gene were also identified, however, these genes are located outside Qlr.nhv-5D.2 interval. Hence, TraesCS5D02G253100 could be the best potential candidate gene for leaf rolling and can be utilized for improving drought tolerance in wheat.

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Fine mapping of the BnUC2 locus related to leaf up-curling and plant semi-dwarfing in Brassica napus

10.21203/rs.2.17555/v1 ◽

2019 ◽

Author(s):

Chengwei Huang ◽

Mao Yang ◽

Danlei Shao ◽

Yangming Wang ◽

Shubei Wan ◽

...

Keyword(s):

Candidate Gene ◽

Plant Height ◽

Ssr Markers ◽

Fine Mapping ◽

Agronomic Traits ◽

Leaf Shape ◽

Planting Density ◽

Lodging Resistance ◽

Leaf Trait ◽

Curled Leaves

Abstract Background Studies of leaf shape development and plant stature have made important contributions to the fields of plant breeding and developmental biology. The optimization of leaf morphology and plant height to improve lodging resistance and photosynthetic efficiency, increase planting density and yield, and facilitate mechanized harvesting is a desirable goal in Brassica napus.Results Here, we investigated a B. napus germplasm resource exhibiting up-curled leaves and a semi-dwarf stature. In progeny populations derived from NJAU5737 and Zhongshuang 11 (ZS11), we found that the up-curled leaf trait was controlled by a dominant locus, BnUC2. We then fine mapped the BnUC2 locus onto an 83.19-kb interval on chromosome A05 using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. We further determined that BnUC2 was a major plant height QTL that explained approximately 70% of the phenotypic variation in two BC5F3 family populations derived from NJAU5737 and ZS11. This result implies that BnUC2 was also responsible for the observed semi-dwarf stature. The fine mapping interval of BnUC2 contained five genes, two of which, BnaA05g16700D (BnaA05.IAA2) and BnaA05g16720D, were revealed by comparative sequencing to be mutated in NJAU5737. This result suggests that the candidate gene mutation (BnaA05g16700D) in the conserved Degron motif GWPPV (P63S) was responsible for the BnUC2 locus. In addition, investigation of agronomic traits in a separation population indicated that plant height, main inflorescence length, and branching height were significantly reduced by BnUC2, whereas yield was not significantly altered. Our findings may provide an effective foundation for plant type breeding in B. napus.Conclusions Using SNP and SSR markers, a dominant locus (BnUC2) related to up-curled leaves and semi-dwarf stature in B. napus has been fine mapped onto an 83.19-kb interval of chromosome A05 containing five genes. The BnaA05g16700D (BnaA05.IAA2) is inferred to be candidate gene responsible for the BnUC2 locus.

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Development and validation of heat-responsive candidate gene and miRNA gene based SSR markers to analysis genetic diversity in wheat for heat tolerance breeding

Molecular Biology Reports ◽

10.1007/s11033-020-06059-1 ◽

2021 ◽

Author(s):

Pradeep Sharma ◽

Geetika Mehta ◽

Shefali ◽

Senthilkumar K. Muthusamy ◽

Sanjay Kumar Singh ◽

...

Keyword(s):

Genetic Diversity ◽

Candidate Gene ◽

Ssr Markers ◽

Heat Tolerance ◽

Mirna Gene ◽

Development And Validation

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Candidate gene based characterization of common bean genotypes

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.78.3.15 ◽

2018 ◽

Vol 78 (3) ◽

Author(s):

Sajad Majeed Zargar ◽

Nancy Gupta ◽

Reetika Mahajan ◽

Susheel Sharma ◽

F. A. Nehvi ◽

...

Keyword(s):

Candidate Gene ◽

Common Bean ◽

Ssr Markers ◽

Genetic Improvement ◽

Power Estimation ◽

Resolving Power ◽

Yield Traits ◽

Marker Index ◽

High Level

A set of 96 common bean genotypes were characterized using 25 candidate gene based SSR markers associated with yield traits. Twenty three SSR markers were found polymorphic and their discriminatory power estimation was performed on the basis of PIC, resolving power and marker index that mainly explain ability of molecular markers to distinguish genotypes. An average of 0.33 PIC was observed where highest value was exhibited by the primer BM184. The primers BM170 and Bmd8 generated four alleles whereas BM170 showed maximum marker index of 1.28 and highest resolving power of 1.89 was found in case of primer BM180. Further, the genotypes were grouped in three major clusters based on DARwin5 software. High level of genetic diversity observed within the genotypes could be used to accelerate genetic improvement of germplasm in common bean targeting yield attributing traits.

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