QTL Analysis for Bread Wheat Seed Size, Shape and Color Characteristics Estimated by Digital Image Processing

Abstract

The size, shape, and color of wheat seeds are important traits that are associated with yield and flour quality (size, shape), nutritional value, and pre-harvest sprouting (coat color). These traits are under multigenic control, and to dissect their molecular and genetic basis, quantitative trait loci (QTL) analysis is used. We evaluated 114 recombinant inbred lines (RILs) in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative, ITMI/MP) grown in 2014 season. We used digital image analysis for seed phenotyping and obtained data for seven traits describing seed size and shape and 48 traits of seed coat color. We identified 212 additive and 34 pairs of epistatic QTLs on all the chromosomes of wheat genome except chromosomes 1A and 5D. Many QTLs were overlapping. We demonstrated that the overlap between QTL regions was low for seed size/shape traits and high for coat color traits. Using the literature and KEGG data, we identified sets of genes in Arabidopsis and rice from the networks controlling seed size and color. Further, we identified 29 and 14 candidate genes for seed size-related loci and for loci associated with seed coat color, respectively.

Cytological and genetic effects of rye chromosomes 1RS and 3R on the wheat-breeding founder parent Chuanmai 42 from southwestern China

“…The QTL on chromosome 3D, which explained more than 50% of the phenotypic variation, was consistent with the location of R-1/TaMyb10(Himi et al 2011), which is associated with the PHS-3D-mediated resistance to pre-harvest sprouting(Lang et al 2021). Few QTLs for SCC were detected on chromosome 5B, with the exception of the QTLs related to seed color characteristics on chromosome 5BL(Arif et al 2022).…”

Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L.

“…We hypothesize the presence of genes within this locus affecting grain color development. Our study's grain color loci did not coincide with those identified by Arif et al, who employed the same seed color estimation method [51]. However, the locus containing the TraesCS7B03G1296800 gene on chromosome 7B, encoding PSY, was previously associated with flour and endosperm color [52,53].…”

“…The digital image processing and color analysis was performed using Seed-Counter application, version for desktop PC [37,38]. A single image per accession was used, since previous work demonstrated no significant differences between mean values of the seed traits obtained for several replicates [51]. Seeds were imaged before sowing in 2021.…”

“…For the markers associated with seed coat color, we selected genes expressed in seeds first. For this purpose, we used data downloaded from the expVIP database, as described previously [51]. Genes were selected with TPM > 1 in seeds ("High level tissue" contains "seed").…”

Determination of the melanin and anthocyanin content in barley grains by digital image analysis using machine learning methods

“…An alternative is the use of digital RGB cameras that produce high-quality images with high spatial and color resolution (Afonnikov et al, 2016;Li et al, 2020;Kolhar, Jagtap, 2023). In this regard, methods for estimating color and textural characteristics of cereal grains based on the analysis of twodimensional images acquired by digital cameras or scanners have recently been intensively developed in the field of grain phenotyping (Komyshev et al, 2020;Sharma et al, 2021;Afonnikov et al, 2022;Arif et al, 2022;Khojastehnazhand, Roostaei, 2022;Wang, Su, 2022).…”