基于ND-FISH和SNP芯片技术实现对小麦遗传背景中华山新麦草染色体的快速鉴定

doi:10.1016/j.jia.2023.02.001

Journal of Integrative Agriculture ›› 2023, Vol. 22 ›› Issue (10): 2934-2948.DOI: 10.1016/j.jia.2023.02.001

基于ND-FISH和SNP芯片技术实现对小麦遗传背景中华山新麦草染色体的快速鉴定

收稿日期:2022-09-19 接受日期:2022-11-14 出版日期:2023-10-20 发布日期:2023-10-07

Rapid identification of Psathyrostachys huashanica Keng chromosomes in wheat background based on ND-FISH and SNP array methods

LI Jia-chuang^{1, 2}^*, LI Jiao-jiao¹^*, ZHAO Li³, ZHAO Ji-xin³, WU Jun³, CHEN Xin-hong³, ZHANG Li-yu¹, DONG Pu-hui¹, WANG Li-ming¹, ZHAO De-hui^{1, 2}, WANG Chun-ping^{1, 2#}, PANG Yu-hui^{1, 2#}

¹College of Agronomy, Henan University of Science and Technology, Luoyang 471023, P.R.China
²The Shennong Laboratory, Henan Provience, Zhengzhou 450002, P.R.China
³ College of Agronomy, Northwest A&F University, Yangling 712100, P.R.China

Received:2022-09-19 Accepted:2022-11-14 Online:2023-10-20 Published:2023-10-07
About author:LI jia-chuang, E-mail: lijiachuang0208@126.com; LI Jiao-jiao, E-mail: 1439491104@qq.com; #Correspondence PANG Yu-hui, E-mail: pangyuhui@aliyun.com; WANG Chun-ping, E-mail: chunpingw@haust.edu.cn * These authors contributed equally to this study.
Supported by:
This study was supported by the National Natural Science Foundation of China (31501301), the National Key Research and Development Plan for the “Thirteenth Five-Year Plan” (2018YFD0100904), the Natural Science Foundation of Henan Province, China (162300410077), and the International Cooperation Project of Henan Province, China (172102410052).

摘要/Abstract

摘要：

华山新麦草(2n=2x=14, NsNs)因具有诸多优异的农艺性状被认为是对普通小麦品种改良而言具有重要价值的野生近缘种。然而，尽管多个小麦-华山新麦草衍生后代的创制为优异性状的转移提供了种质资源基础，但小麦背景中华山新麦草染色体鉴定方法的滞后限制了对这些衍生后代的研究。本研究开发了三条高效非变性荧光原位杂交（ND-FISH）探针，其中HS-TZ3和HS-TZ4能特异性地结合华山新麦草染色体端粒区域，HS-TZ5可以和染色体着丝粒区域结合。华山新麦草染色体的FISH核型图和模式图被分别构建，以便于区分衍生系中所导入华山新麦草染色体的同源群归属。具体而言，染色体1Ns和2Ns在短臂和长臂上有相反的荧光信号，3Ns、4Ns和7Ns有叠加的双色荧光信号，5Ns和6Ns仅在短臂有荧光信号，7Ns在长臂的中间区域也有荧光信号。此外，评估了在不同组合方式下利用低密度单核苷酸多态性(SNP)芯片鉴定外源导入系的效果。结果表明最佳的模式是统计分析每条染色体上SNP位点的纯合率，15K SNP芯片可以广泛应用于附加系、代换系和易位系的鉴定，而40K SNP芯片在小麦和外源染色体易位区段的鉴定中最准确。本研究提供了基于ND-FISH和SNP芯片识别小麦背景中华山新麦草染色体同源群归属的简便方法，对于小麦-华山新麦草衍生系的高效鉴别和Ns染色体的进一步利用具有重要意义。

Abstract:

Psathyrostachys huashanica Keng (2n=2x=14, NsNs) is regarded as a valuable wild relative species for common wheat cultivar improvement because of its abundant beneficial agronomic traits. However, although the development of many wheat–P. huashanica-derived lines provides a germplasm base for the transfer of excellent traits, the lag in the identification of P. huashanica chromosomes in the wheat background has limited the study of these lines. In this study, three novel nondenaturing fluorescence in situ hybridization (ND-FISH)-positive oligo probes were developed. Among them, HS-TZ3 and HS-TZ4 could specifically hybridize with P. huashanica chromosomes, mainly in the telomere area, and HS-CHTZ5 could hybridize with the chromosomal centromere area. We sequentially constructed a P. huashanica FISH karyotype and idiogram that helped identify the homologous groups of introduced P. huashanica chromosomes. In detail, 1Ns and 2Ns had opposite signals on the short and long arms, 3Ns, 4Ns, and 7Ns had superposed two-color signals, 5Ns and 6Ns had fluorescent signals only on their short arms, and 7Ns had signals on the intercalary of the long arm. In addition, we evaluated different ways to identify alien introgression lines by using low-density single nucleotide polymorphism (SNP) arrays and recommended the SNP homozygosity rate in each chromosome as a statistical pattern. The 15K SNP array is widely applicable for addition, substitution, and translocation lines, and the 40K SNP array is the most accurate for recognizing transposed intervals between wheat and alien chromosomes. Our research provided convenient methods to distinguish the homologous group of P. huashanica chromosomes in a common wheat background based on ND-FISH and SNP arrays, which is of great significance for efficiently identifying wheat–P. huashanica-derived lines and the further application of Ns chromosomes

Key words: Psathyrostachys huashanica , Ns chromosomes , ND-FISH , SNP array , common wheat

LI Jia-chuang, LI Jiao-jiao, ZHAO Li, ZHAO Ji-xin, WU Jun, CHEN Xin-hong, ZHANG Li-yu, DONG Pu-hui, WANG Li-ming, ZHAO De-hui, WANG Chun-ping, PANG Yu-hui. 基于ND-FISH和SNP芯片技术实现对小麦遗传背景中华山新麦草染色体的快速鉴定[J]. Journal of Integrative Agriculture, 2023, 22(10): 2934-2948.

LI Jia-chuang, LI Jiao-jiao, ZHAO Li, ZHAO Ji-xin, WU Jun, CHEN Xin-hong, ZHANG Li-yu, DONG Pu-hui, WANG Li-ming, ZHAO De-hui, WANG Chun-ping, PANG Yu-hui. Rapid identification of Psathyrostachys huashanica Keng chromosomes in wheat background based on ND-FISH and SNP array methods[J]. Journal of Integrative Agriculture, 2023, 22(10): 2934-2948.

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基于ND-FISH和SNP芯片技术实现对小麦遗传背景中华山新麦草染色体的快速鉴定

Rapid identification of Psathyrostachys huashanica Keng chromosomes in wheat background based on ND-FISH and SNP array methods

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