A haplotype-led approach to increase the precision of wheat breeding.
A haplotype-led approach to increase the precision of wheat breeding.
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DOI：
10.1038/s42003-020-01413-2
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发表时间：
2020-11-25
影响因子：
5.9
通讯作者：
Uauy C
中科院分区：
文献类型：
--
作者：
Brinton J;Ramirez-Gonzalez RH;Simmonds J;Wingen L;Orford S;Griffiths S;10 Wheat Genome Project;Haberer G;Spannagl M;Walkowiak S;Pozniak C;Uauy C
作物生产力必须以前所未有的速度增长，以满足不断增长的世界人口的需求。利用自然变异进行作物遗传改良在提高生产力方面发挥着核心作用。虽然目前的基因组技术可用于高通量鉴定遗传变异，但缺乏以有针对性的系统方式有效利用这种遗传潜力的方法。在这里，我们开发了一种基于单倍型的方法来识别遗传多样性的作物改良使用基因组组件从15个面包小麦（小麦）品种。我们使用严格的标准来识别相同的单倍型，并将其与几乎相同的序列（约99.95%的同一性）区分开来。我们发现每个品种与其他测序的品种共享约59%的基因组，并且我们检测到所有小麦染色体上存在包含数百至数千个基因的扩展单倍型块。我们发现，基因序列本身是不足以完全区分单倍型，因为通常使用的基于阵列的基因分型芯片，由于其基因中心的设计。我们成功地使用这种方法集中发现新的单倍型从地方品种收集和记录其在现代面包小麦性状改良的潜力。这项研究为确定和利用单倍型提供了一个框架，以提高小麦育种的效率和精度，从而优化这一关键作物的农艺性状。Brinton，Uauy及其同事利用10+小麦基因组计划的基因组数据开发了一种有用的工具，用于研究和产生新的小麦品种。该框架利用小麦单倍型的先进开发，为小麦育种带来新的精度和效率。
Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for efficiently exploiting this genetic potential in a targeted, systematic manner are lacking. Here, we developed a haplotype-based approach to identify genetic diversity for crop improvement using genome assemblies from 15 bread wheat (Triticum aestivum) cultivars. We used stringent criteria to identify identical-by-state haplotypes and distinguish these from near-identical sequences (~99.95% identity). We showed that each cultivar shares ~59 % of its genome with other sequenced cultivars and we detected the presence of extended haplotype blocks containing hundreds to thousands of genes across all wheat chromosomes. We found that genic sequence alone was insufficient to fully differentiate between haplotypes, as were commonly used array-based genotyping chips due to their gene centric design. We successfully used this approach for focused discovery of novel haplotypes from a landrace collection and documented their potential for trait improvement in modern bread wheat. This study provides a framework for defining and exploiting haplotypes to increase the efficiency and precision of wheat breeding towards optimising the agronomic performance of this crucial crop. Brinton, Uauy and colleagues utilize genomic data from the 10+ Wheat Genome Project to develop a useful tool for studying and generating new wheat cultivars. This framework uses advanced exploitation of wheat haplotypes to bring newfound precision and efficiency to wheat breeding.
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影响因子：
13.8
作者：
Allen AM;Winfield MO;Burridge AJ;Downie RC;Benbow HR;Barker GL;Wilkinson PA;Coghill J;Waterfall C;Davassi A;Scopes G;Pirani A;Webster T;Brew F;Bloor C;Griffiths S;Bentley AR;Alda M;Jack P;Phillips AL;Edwards KJ
通讯作者：
Edwards KJ
影响因子：
48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
通讯作者：
Holmes SP
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
56.9
作者：
Gabriel, SB;Schaffner, SF;Altshuler, D
通讯作者：
Altshuler, D
DOI：
10.1093/bioinformatics/btq475
发表时间：
2010-10-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Goto N;Prins P;Nakao M;Bonnal R;Aerts J;Katayama T
通讯作者：
Katayama T