小麥穗部及其結構是提高糧食產量的重要組成部分。近年來，在作物中發現了一些控制穗部形態的基因，小麥穗及其結構是提高糧食產量的關鍵組成部分。最近，在作物中的研究鑑定了一些控制穗部形態的基因，而小麥中大多數為穗長和小穗數等性狀的數量性狀。
本文作者Muqaddasi等人於2019年9月在Scientific Reports發表了題為‘TaAPO-A1, an ortholog of riceABERRANT PANICLEORGANIZATION 1, is associated with total spikelet number per spike in eliteeuropean hexaploid winter wheat (Triticum aestivum L.) varieties’的文章。作者根據518種歐洲優質冬小麥品種的穗長和花期研究了總小穗數的遺傳基礎以及其他性狀。基於39908個SNP標記的全基因組關聯分析揭示了小麥染色體2D、7A 和 7B 上的小穗數QTL、5A上的穗長QTL和2D上的開花時間QTL，其中2D-QTL 是基因Ppd-D1的功能標記。總小穗數的7A-QTL物理區域顯示存在與水稻中APO1的小麥直系同源基因TaAPO-A1，APO1是一種水稻基因，可正向調控穗部小穗數。對TaAPO-A1同源基因的分析表明，它是一個高度保守的基因，對花的發育十分重要，存在於多種植物中。透過對小麥中TaAPO-A1基因型的研究發現，TaAPO-A1在保守的F-box結構域存在多型性，定義了兩個單倍型。在多型性位點開發的 KASP 標記顯示TaAPO-A1與總小穗數顯著相關。此外，TaAPO-A1等位基因在穗長和籽粒產量方面存在差異值較低但顯著的差異。本文對透過小麥資源在遺傳分析鑑定重要性狀的候選基因方面具有重要作用。
結果
1、每穗總小穗數與穗長、花期和籽粒產量呈極顯著正相關
Figure1.Distributionand correlation of the investigated traits in a panel of 518 elite Europeanwinter wheat varieties.
Table 1.Summary statistics of the investigated traits,namely total spikelet number (TSN) per spike, spike length (SL; cm), floweringtime (FT), and grain yield (GY;).
2、高密度標記陣列揭示了歐洲優質冬小麥中不存在明顯的亞群和急劇的連鎖不平衡衰減
Figure2. Principal component (PC) analysis on the wheatmarker loci combined from the 35k and 90k single nucleotide polymorphismarrays.
Figure 3. Genome-wide decay of linkage disequilibrium (LD;r2) as a function of genetic map distance (cM) between the marker loci in thepopulation of European winter wheat varieties.
3、GWAS 鑑定了歐洲冬小麥 7A 號染色體上對小穗數影響顯著的 QTL
Figure 4. Manhattan plot shows the distribution ofmarker
significance−log10(P − value)along the chromosomes.
Figure 5.Quantile-quantile plot showing the distribution ofobserved versus expected (red dashed line) −log10(P − value).
Figure 6.Allele-wise phenotypic distribution of the mostsignificant markers and the KASP marker for TaAPO-A1 associated with TSN
Figure 7.Allele-wise phenotypic distribution of the mostsignificant markers and the KASP marker for TaAPO-A1 associated with Grain yield
4、染色體7A-QTL的顯著物理區域包含TaAPO-A1-一個小麥小穗數的可能候選基因
Figure 8.Significant genetic region on chromosome 7A for TSNin wheat. The gray vertical dashed lines mark the highly significant genetic region. Significant physical region on chromosome 7Afor TSN in wheat. The gray vertical dashed lines mark the highly significantphysical region
5、TaAPO-A1基因的KASP標記與小麥品種的小穗數呈顯著相關
Figure 9.Gene structure of the TaAPO-A1.
Allele-wisephenotypic distribution of the most significant markers and the KASP marker for TaAPO-A1 associated with TSN
Figure 10.Allele-wise phenotypic distribution of the mostsignificant markers and the KASP marker for TaAPO-A1 associated with Spike length, Flowering time, and Grain yield.
Figure 11. Pairwiselinkage disequilibrium (LD; r2) among the marker loci (including the KASPmarker for the gene TaAPO-A1present in the significant genetic regionof TSN on chromosome 7A in wheat.
6、系統發育分析表明，擬南芥中 UFO的直系同源物 TaAPO-A1在陸地植物物種中是保守的。
Figure12. Maximum likelihood phylogenetic tree of TaAPO-A1orthologous proteins across terrestrial plant species. Bootstrap values areindicated along the braches.
總結：本文的結果表明，隨著現代基因組工具（例如小麥參考序列）的可用性以及對 10+ 小麥基因組計劃的訪問，從表型到候選基因的過程大大縮短。然而，可靠的遺傳分析，包括適當的群體定位，準確和高密度的基因分型，以及適當的表型分析是檢測可以推斷出致病基因的重要 QTL 區域的先決條件。
來源：Scientificreports，僅用於學術分享，轉載註明來處。若有侵權，請聯絡刪除或修改。
原文連結：https://doi.org/10.1038/s41598-019-50331-9
翻譯：楊瑤瑤 稽核：丁浦洋
