A Pseudo-near isogenic F2 population strategy for rapid QTL cloning

Ahmed Sherif; Bo Zhang; Bi Wu; Yong Hu; Shuangle Li; Xiangchun Zhou; Ali Mahmoud Elbadri; Mostafa Elshenawy; Mahmoud El M El-Badawy; Ibrahim O Hassan; Sedhom A Sedhom; Mahmoud Abo-Yousef; Mohammed Ayaad; Yongzhong Xing

doi:10.1007/s11032-023-01408-x

A Pseudo-near isogenic F₂ population strategy for rapid QTL cloning

Mol Breed. 2023 Jul 25;43(8):61. doi: 10.1007/s11032-023-01408-x. eCollection 2023 Aug.

Authors

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China.
² Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Sakha, 33717 Egypt.
³ Agronomy Department, Faculty of Agriculture, Benha University, Qalyubia Governorate, Benha, 13736 Egypt.
⁴ Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo, 13759 Egypt.

PMID: 37496827
PMCID: PMC10366042 (available on 2024-07-25)
DOI: 10.1007/s11032-023-01408-x

Abstract

Near isogenic F₂ (NIF₂) population frequently developed by conventional backcross has dramatically contributed to QTL identification in plants. Developing such a NIF₂ population is time-consuming. Thus, it is urgent to rapidly produce a NIF₂ population for QTL cloning. Here, we proposed a rapid QTL cloning strategy by generating a Pseudo-near isogenic F₂ population (Pseudo-NIF₂), which segregates at the target QTL but is fixed at other QTLs for the target trait. Nineteen QTLs for GL, GW, and TGW were detected in the F₂ population from the cross between Zhenshan 97 and Egy316. To verify the efficiency of Pseudo-NIF₂ in QTL quick cloning, the novel moderate QTL qGL10.1 which explained 9.1% and 5.6% of grain length variation in F₂ and F_2:3 populations was taken as an example. An F₂ plant (F₂-120), which segregated at qGL10.1 but fixed at other 8 QTLs for grain length, was screened to generate a Pseudo-NIF₂ population by selfing cross. In the Pseudo-NIF₂ population, the segregation ratio of plants with long grains to short grains fits 3:1, indicating that one gene controlled the variation of grain length. Based on the Pseudo-NIF₂ and its progeny, qGL10.1 was fine mapped to a 19.3-kb region, where a gene OsMADS56 was verified as the candidate by functional polymorphism between parental alleles. Pseudo-NIF₂ strategy is a rapid way for QTL cloning, which saves 3 to 4 cropping seasons compared to the conventional way. Applying the method for cloning QTL with moderate or major effects is promising.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01408-x.

Keywords: Grain length; Primary QTL mapping; Pseudo-near isogenic F2; Rapid QTL cloning.

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