Homologous haplotypes, expression, genetic effects and geographic distribution of the wheat yield gene TaGW2

Abstract

BackgroundTaGW2-6A, cloned in earlier research, strongly influences wheat grain width and TKW. Here, we mainly analyzed haplotypes of TaGW2-6B and their effects on TKW and interaction with haplotypes at TaGW2-6A.ResultsAbout 2.9 kb of the promoter sequences of TaGW2-6B and TaGW2-6D were cloned in 34 bread wheat cultivars. Eleven SNPs were detected in the promoter region of TaGW2-6B, forming 4 haplotypes, but no divergence was detected in the TaGW2-6D promoter or coding region. Three molecular markers including CAPS, dCAPS and ACAS, were developed to distinguish the TaGW2-6B haplotypes. Haplotype association analysis indicated that TaGW2-6B has a stronger influence than TaGW2-6A on TKW, and Hap-6B-1 was a favored haplotype increasing grain width and weight that had undergone strong positive selection in global wheat breeding. However, clear geographic distribution differences for TaGW2-6A haplotypes were found; Hap-6A-A was favored in Chinese, Australian and Russian cultivars, whereas Hap-6A-G was preferred in European, American and CIMMYT cultivars. This difference might be caused by a flowering and maturity time difference between the two haplotypes. Hap-6A-A is the earlier type. Haplotype interaction analysis between TaGW2-6A and TaGW2-6B showed additive effects between the favored haplotypes. Hap-6A-A/Hap-6B-1 was the best combination to increase TKW. Relative expression analysis of the three TaGW2 homoeologous genes in 22 cultivars revealed that TaGW2-6A underwent the highest expression. TaGW2-6D was the least expressed during grain development and TaGW2-6B was intermediate. Diversity of the three genes was negatively correlated with their effect on TKW.ConclusionsGenetic effects, expression patterns and historic changes of haplotypes at three homoeologous genes of TaGW2 influencing yield were dissected in wheat cultivars. Strong and constant selection to favored haplotypes has been found in global wheat breeding during the past century. This research also provides a valuable case for understanding interaction of genes that control complex traits in polyploid species.

A yield-associated gene TaCWI, in wheat: its function, selection and evolution in global breeding revealed by haplotype analysis

“…Evidence of selection was supported by changes in haplotype frequencies in the last 60 years. We found differences between haplotypes at the same locus influence selection time and intensity Qin et al 2014). S6).…”

The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice

“…Among these 30 genes, 26 are located in the candidate region mapped by at least one method (SLM, JLM, and GWAS) in the RIL populations and five were found to be significantly associated with kernel traits by candidate gene association mapping in a large association panel. Given the conserved functions of many of the known genes for kernel development in maize, rice, and wheat (Su et al, 2011;Hong et al, 2014;Qin et al, 2014;Jaiswal et al, 2015;Wang et al, 2015Wang et al, , 2016Ma et al, 2016;Simmonds et al, 2016), these genes represent additional candidates for kernel development across various species.…”

“…Similarly, Liu et al (2015) showed that GS5 contributes to kernel size variation in maize as well as in rice. Notably, the wheat orthologs of rice GW2 and GS5 also were associated significantly with wheat kernel size and weight (Su et al, 2011;Hong et al, 2014;Qin et al, 2014;Jaiswal et al, 2015;Wang et al, 2015Wang et al, , 2016Ma et al, 2016;Simmonds et al, 2016). In addition to GS3, GW2, and GS5, many other genes controlling rice kernel size/weight have been cloned, such as genes involved in G-protein signaling (DEP1 and D1) and genes from phytohormone pathways (DST and Gn1a for cytokinin; D11, SRS5, D61, qGL3, and SMG1 for brassinosteroid; and TGW6 for auxin).…”

Isolation and characterization of the TaSnRK2.10 gene and its association with agronomic traits in wheat (Triticum aestivum L.)

“…10 gene had functions that affect the TGW, PH and SL during the maturity stage. To date, some grain weight genes have been isolated, such as Ppd-D1 [56], CKX6-D1 [57], GS1a [11], GW2 [8, 58–59], GS-D1 [60], Sus [9, 61], GASR7 [62–63], TEF-7 [64], CWI [65], and 1-FEH-w3 [66–67]. Using sequence comparison and the analysis of protein domains with PROSITE (http://prosite.expasy.org/), we found that TaSnRK2 .…”