RESUMO
Genetic improvement of seed yield per plant (SY) is one of the major objectives in Brassica napus breeding programme. SY, being a complex quantitative trait is directly and indirectly influenced by yield-component traits such as siliqua length (SL), number of seeds per siliqua (NSS), and thousand seed weight (TSW). Therefore, concurrent improvement in SL, NSS and TSW can lead to higher SY in B. napus. This study was conducted to identify significant SNPs and putative candidate genes governing SY and its component traits (SL, NSS, TSW). All these traits were evaluated in a diverse set of 200 genotypes representing diversity from wide geographical locations. Of these, a set of 125 genotypes were chosen based on pedigree diversity and multi-location trait variation for genotyping by sequencing (GBS). Best linear unbiased predictors (BLUPs) of all the traits were used for genome-wide association study (GWAS) with 85,126 SNPs obtained from GBS. A total of 16, 18, 27 and 18 SNPs were found to be significantly associated for SL, NSS, TSW and SY respectively. Based on linkage disequilibrium decay analysis, 150 kb genomic region flanking the SNP was used for the identification of underlying candidate genes for each test trait. Important candidate genes involved in phytohormone signaling (WAT1, OSR1, ARR8, CKX1, REM7, REM9, BG1) and seed storage proteins (Cruciferin) were found to have significant influence on seed weight and yield. Genes involved in sexual reproduction and fertilization (PERK7, PERK13, PRK3, GATA15, NFD6) were found to determine the number of seeds per siliqua. Several genes found in this study namely ATS3A, CKX1, SPL2, SPL6, SPL9, WAT1 showed pleiotropic effect with yield component traits. Significant SNPs and putative candidate genes identified for SL, NSS, TSW and SY could be used in marker-assisted breeding for improvement of crop yield in B. napus. Genotypes identified with high SL, NSS, TSW and SY could serve as donors in crop improvement programs in B. napus. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01060-9.
RESUMO
α-amylase is an important enzyme involved in starch degradation to provide energy to the germinating seedling. The present study was conducted to reveal structural and functional evolution of this gene among higher plants. Discounting polyploidy, most plant species showed only a single copy of the gene making multiple isoforms in different tissues and developmental stages. Genomic length of the gene ranged from 1472 bp in wheat to 2369 bp in soybean, and the size variation was mainly due to differences in the number and size of introns. In spite of this variation, the intron phase distribution and insertion sites were mostly conserved. The predicted protein size ranged from 414 amino acid (aa) in soybean to 449aa in Brachypodium. Overall, the protein sequence similarity among orthologs ranged from 56.4 to 97.4 %. Key motifs and domains along with their relative distances were conserved among plants although several species, genera, and class specific motifs were identified. The glycosyl hydrolase superfamily domain length varied from 342aa in soybean to 384aa in maize and sorghum while length of the C-terminal ß-sheet domain was highly conserved with 61aa in all monocots and Arabidopsis but was 59aa in soybean and Medicago. Compared to rice, 3D structure of the proteins showed 89.8 to 91.3 % similarity among the monocots and 72.7 to 75.8 % among the dicots. Sequence and relative location of the five key aa required for the ligand binding were highly conserved in all species except rice.