Identification of TaPPH-7A haplotypes and development of a molecular marker associated with important agronomic traits in common wheat

Abstract

Background Premature senescence of flag leaf severely affects wheat yield and quality. Chlorophyll (Chl) degradation is the most obvious symptom during leaf senescence and catalyzed by a series of enzymes. Pheophytin pheophorbide hydrolase (Pheophytinase, PPH) gene encodes a Chl degradation hydrolase. Results In this study, the coding, genomic and promoter sequences of wheat TaPPH-A gene were cloned. The corresponding lengths were 1467 bp, 4479 bp and 3666 bp, respectively. Sequence structure analysis showed that TaPPH-A contained five exons and four introns. After the multiple sequences alignment of TaPPH-A genome from 36 accessions in a wheat diversity panel, four SNPs and one 2-bp InDel were observed, which formed two haplotypes, TaPPH-7A-1 and TaPPH-7A-2 . Based on the SNP at 1299 bp (A/G), a molecular marker TaPPH-7A -dCAPS was developed to distinguish allelic variation (A/G). Using the molecular markers, 13 SSR, and 116 SNP markers, a linkage map of chromosome 7A were integrated. TaPPH-A was mapped on the chromosome region flanked by Xwmc9 (0.94 cM) and AX-95634545 (1.04 cM) on 7A in a DH population. Association analysis between TaPPH-7A allelic variation and agronomic traits found that TaPPH-7A was associated with TGW in 11 of 12 environments and Chl content at grain-filling stage under drought stress using Population 1 consisted of 323 accessions. The accessions possessed TaPPH-7A-1 (A) had higher TGW and Chl content than those possessed TaPPH-7A-2 (G), thus TaPPH-7A-1 (A) was a favorable allelic variation. By analyzing the frequency of favorable allelic variation TaPPH-7A-1 (A) in Population 2 with 157 landraces and Population 3 with 348 modern cultivars, we found it increased from pre-1950 (0) to 1960s (54.5%), then maintained a relatively stable level about 56% from 1960s to 1990s. Conclusion These results suggested the favorable allelic variation TaPPH-7A-1 (A) should be valuable in enhancing grain yield by improving the source (chlorophyll content) and sink (the developing grain) simultaneously. Furthermore, the newly developed molecular marker TaPPH-7A -dCAPS could be integrated into a breeding kit of screening high TGW wheat for marker-assisted selection. Electronic supplementary material The online version of this article (10.1186/s12870-019-1901-0) contains supplementary material, which is available to authorized users.

Development and Exploitation of KASP Assays for Genes Underpinning Drought Tolerance Among Wheat Cultivars From Pakistan

“…The given Pakistani wheat germplasm had high frequencies of unfavorable allelic variations for TaMOC-7A and TaPARG-2A, suggesting the potential of favorable haplotype introgression through functional markers. Previously, selection pressure was observed on TaSnRK2.3-1A/B (Miao et al, 2017), TaSnRK2.9-5A (Ur Rehman et al, 2019), TaSAP-7B (Wang et al, 2018), TaMOC-7A , TaLTPs-1A , TaPARG-2A (Li B. et al, 2016), and TaPPH-7A (Wang et al, 2019) favorable allelic variations in Chinese wheat cultivars where the frequencies of favored haplotypes had gradually increased from the beginning of the last century. Both PIC and H e values were higher in tetraploid wheat as compared to Pakistani hexaploid wheat.…”

“…TaSnRK2.3-1A/1B (Miao et al, 2017), TaSnRK2.9-5A (Ur Rehman et al, 2019), TaPARG-2A (Li B. et al, 2016), TaSAP-7B (Wang et al, 2018), TaPPH-7A (Wang et al, 2019), and TaMOC1-7A are associated with higher grain yield under water stress conditions. TaSnRK2.8-5A associated with higher seedling biomass under normal conditions and water-soluble carbohydrates under limited irrigation conditions (Zhang et al, 2013), TaLTPs-1A associated with ideal plant height under drought conditions , and TaDreb-B1 (Wei et al, 2009) and 1-feh w3 are also reported as drought toleranceconferring genes.…”

“…3 -1A/1B ( Miao et al, 2017 ), TaSnRK2 . 9 -5A ( Ur Rehman et al, 2019 ), TaPARG -2A ( Li B. et al, 2016 ), TaSAP -7B ( Wang et al, 2018 ), TaPPH -7A ( Wang et al, 2019 ), and TaMOC1 -7A ( Zhang B. et al, 2015 ) are associated with higher grain yield under water stress conditions. TaSnRK2 .…”

Root and canopy traits and adaptability genes explain drought tolerance responses in winter wheat

“…Transcription factors like DREB control the expression of several functional genes responsible for plant tolerance to drought, and have been proposed for use in plant improvement for drought tolerance [ 33 ]. Similarly, TaTEF-7A is transcript elongation factor gene responsible for grain number per spike [ 34 ], thousand grain weight and chlorophyll content at grain-filling stage under drought stress [ 35 ]. The gene TaPRR73 was found to be regulation of flowering date and can be used in breeding to develop cultivars adaptable for different geographical areas [ 36 ].…”

Root and canopy traits and adaptability genes explain drought tolerance mechanism in winter wheat

“…Transcription factors like DREB known to control the expression of several functional genes responsible for plant tolerance to drought, high-salt and cold stress and have been propose to use in plant improvement for stress tolerance (28). Similarly, TaTEF-7A is transcript elongation factor gene responsible for number per spike (29) and thousand grain weight under (30). The gene TaPRR73 was found to be regulation of flowering date and can be used in breeding to develop cultivars adaptable for different geographical areas (31).…”