Mapping of important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut (Arachis hypogaea L.)

Abstract

A mapping population of recombinant inbred lines (RILs) derived from TMV 2 and its mutant, TMV 2-NLM was employed for mapping important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut. Single nucleotide polymorphism and copy number variation using RAD-Sequencing data indicated very limited polymorphism between TMV 2 and TMV 2-NLM. But phenotypically they differed significantly for many taxonomic and productivity traits. Also, the RIL population showed significant variation for a few additional agronomic traits. A genetic linkage map of 1,205.66 cM was constructed using 91 genic and non-genic Arachis hypogaea transposable element (AhTE) markers. Using single marker analysis and QTL analysis, the markers with high phenotypic variance explained (PVE) were identified for branching pattern (32.3%), number of primary and secondary branches (19.9% and 28.4%, respectively), protein content (26.4%), days to 50% flowering (22.0%), content of oleic acid (15.1%), test weight (13.6%) and pod width (12.0%). Three genic markers (AhTE0357, AhTE0391, AhTE0025) with Arachis hypogaea miniature inverted-repeat transposable element (AhMITE1) activity in the genes Araip.TG1BL (B02 chromosome), Aradu.7N61X (A09 chromosome) and Aradu.7065G (A07 chromosome), respectively showed strong linkage with these taxonomic, productivity and quality traits. Since TMV 2 and TMV 2-NLM differed subtly at DNA level, the background noise in detecting the marker-trait associations was minimum; therefore, the markers identified in this study for the taxonomic and productivity traits may be significant and useful in peanut molecular breeding.

Profiling of Nutraceuticals and Proximates in Peanut Genotypes Differing for Seed Coat Color and Seed Size

“…This may be due to the biallelic nature of AhTE markers and also the type of population which consist of diverse genotypes. This finding was in accordance with previous peanut studies (50,51). About 41 out of 100 AhTE markers screened across 60 genotypes were found to be polymorphic.…”

“…AhTE markers have shown greater potential to differentiate the genotypes in groundnut (42,43,46). As AhTE markers can be easily screened on agarose gel through electrophoresis, they have been utilized in trait mapping using linkage and association mapping approaches (41)(42)(43)(47)(48)(49)(50)(51). The candidate genes or genomic regions governing the nutritional traits are presently not available.…”

Identification of main effect and epistatic quantitative trait loci for morphological and yield-related traits in peanut (Arachis hypogaea L.)

“…There have been some reports of using epistatic QTLs in plant breeding to confirm the universality and the importance of epistasis between QTLs and provide useful information for improving plant height via heterosis and QTL pyramiding in rice (Zhu et al 2015). Most of the QTL analysis conducted for agronomic traits in peanut till date reported just M-QTLs and therefore provided no idea on environment interactions (Kolekar et al 2016;Hake et al 2017;Luo et al 2017a;Luo et al 2017b). However, few studies provided information on both type of QTLs (M-QTLs and E-QTLs) for traits such as drought-related traits (Ravi et al 2011;Gautami et al 2012), fatty acids (Pandey et al 2014b;Wang et al 2015), and pod-and kernel-related traits (Chen et al 2016a).…”

Nested‐association mapping (NAM)‐based genetic dissection uncovers candidate genes for seed and pod weights in peanut (Arachis hypogaea)

“…These populations were genotyped using the Axiom_ Arachis 58K SNP array (Clevenger et al , ; Pandey et al , ) and phenotyped for 2 years of 2015 and 2016, followed by QTL linkage mapping and genomewide association study (GWAS). This report demonstrates the utility and power of the NAM approach in peanut by producing a high‐density genetic map and identifying QTLs and SNP–trait associations (STAs) with greater significance than those observed in biparental populations (Chavarro et al , ; Hake et al , ; Luo et al , ) in pod and seed weights. These identified markers and candidate genes shed light on potential mechanisms controlling pod and seed development in peanut and may serve as useful markers in molecular breeding programs.…”

“…Quantitative trait locus (QTL) mapping studies have been used in peanut for genetic dissection of complex traits, mainly based on biparental populations (Guo et al , ; Kumar et al , ; Pandey et al , ; Wang et al , ), including peanut pod size and weight (Chavarro et al , ; Hake et al , ; Luo et al , ). Multiparental mapping populations or next‐generation mapping populations, such as NAM (nested‐association mapping) and MAGIC (Multi‐parent Advanced Generation Inter‐Cross), have already shown their potential in maize (Yu et al , ), wheat (Mackay et al , ) and soybean (Xavier et al , ).…”