Dataset Information

QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat.

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.

SUBMITTER: Verma A

PROVIDER: S-EPMC7596552 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat.

Verma Aakriti A Niranjana M M Jha S K SK Mallick Niharika N Agarwal Priyanka P Vinod

Scientific reports 20201029 1

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 ...[more]

PMID: 33122772

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Project description:BackgroundRolling of leaves (RL) is a phenomenon commonly found in grasses. Morphology of the leaf is an important agronomic trait in field crops especially in rice; therefore, majority of the rice breeders are interested in RL. There are only few studies with respect to RL of wheat and barley; however, the information regarding the genetic base of RL with respect to the shape of leaf in rye is lacking. To the best of our knowledge, this is the first study on the localization of loci controlling RL on high density consensus genetic map of rye.ResultsGenotypic analysis led to the identification of 43 quantitative trait loci (QTLs) for RL, grouped into 28 intervals, which confirms the multigenic base of the trait stated for wheat and rice. Four stable QTLs were located on chromosomes 3R, 5R, and 7R. Co-localization of QTL for RL and for different morphological, biochemical and physiological traits may suggests pleiotropic effects of some QTLs. QTLs for RL were associated with QTLs for such morphological traits as: grain number and weight, spike number per plant, compactness of spike, and plant height. Two QTLs for RL were found to coincide with QTLs for drought tolerance (4R, 7R), two with QTLs for heading earliness (2R, 7R), one with α-amylase activity QTL (7R) and three for pre-harvest sprouting QTL (1R, 4R, 7R). The set of molecular markers strongly linked to RL was selected, and the putative candidate genes controlling the process of RL were identified. Twelve QTLs are considered as linked to candidate genes on the base of DArT sequences alignment, which is a new information for rye.ConclusionsOur results expand the knowledge about the network of QTLs for different morphological, biochemical and physiological traits and can be a starting point to studies on particular genes controlling RL and other important agronomic traits (yield, earliness, pre-harvest sprouting, reaction to water deficit) and to appoint markers useful in marker assisted selection (MAS). A better knowledge of the rye genome and genes could both facilitate rye improvement itself and increase the efficiency of utilizing rye genes in wheat breeding.

Project description:There is a significant yield reduction in the wheat crop as a result of different biotic and abiotic stresses, and changing climate, among them moisture deficit stress and leaf rust are the major ones affecting wheat worldwide. HD3086 is a high-yielding wheat variety that has been released for commercial cultivation under timely sown irrigated conditions in the Indo-Gangetic plains of India. Variety HD3086 provides a good, stable yield, and it is the choice of millions of farmers in India. It becomes susceptible to the most prevalent pathotypes 77-5 and 77-9 of Puccinia triticina (causing leaf rust) in the production environment and its potential yield cannot be realized under moisture deficit stress. The present study demonstrates the use of a marker-assisted back cross breeding approach to the successful transfer of leaf rust resistance gene Lr24 and QTLs linked to moisture deficit stress tolerance in the background of HD3086. The genotype HI1500 was used as a donor parent that possesses leaf rust-resistant gene Lr24, which confers resistance against the major pathotypes found in the production environment. It possesses inbuilt tolerance under abiotic stresses with superior quality traits. Foreground selection for gene Lr24 and moisture deficit stress tolerance QTLs linked to Canopy temperature (CT), Normal Differential Vegetation Index (NDVI) and Thousand Kernel Weight (TKW) in different generations of the backcrossing and selection. In BC2F2, foreground selection was carried out to identify homozygous lines based on the linked markers and were advanced following pedigree based phenotypic selection. The selected lines were evaluated against P. triticina pathotypes 77-5 and 77-9 under controlled conditions. Recurrent parent recovery of the selected lines ranged from 78-94%. The identified lines were evaluated for their tolerance to moisture stress under field conditions and their resistance to rust under artificial epiphytotic conditions for two years. In BC2F5 generation, eight positive lines for marker alleles were selected which showed resistance to leaf rust and recorded an improvement in component traits of moisture deficit stress tolerance such as CT, NDVI, TKW and yield compared to the recurrent parent HD3086. The derived line is named HD3471 and is nominated for national trials for testing and further release for commercial cultivation.

Dataset Information

QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat.

Publications

QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat.

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