China maps cotton's evolutionary secrets to build better crops

BEIJING -- Chinese scientists have constructed the most comprehensive genetic map of the world's primary cotton crop to date. This breakthrough not only sheds light on how the plant has evolved but also uncovers previously hidden genetic traits that could help create more resilient and productive cotton varieties.

The research, published in Nature Genetics recently, was conducted by a team led by Li Fuguang and Yang Zhao'en from the Institute of Cotton Research of the Chinese Academy of Agricultural Sciences.

It addresses a critical bottleneck in global cotton production: intensive cultivation and selective breeding have drastically narrowed the genetic diversity of upland cotton, which supplies over 95 percent of the world's natural fiber. This makes crops more vulnerable to diseases, pests, and climate change while limiting further quality improvements, the research team told Xinhua on Monday.

To find new genetic material for breeding, the team built what they term a "super pangenome" -- an extensive genetic library compiled from 107 representative varieties of upland cotton.

This powerful tool enabled them to identify large-scale structural variations in the plant's DNA, including significant rearrangements, exchanges, and inversions of chromosomal segments that drive adaptation.

A landmark discovery was the identification of a specific large-scale chromosomal exchange. This genetic signature indicates that modern cotton originated from a surprisingly narrow lineage in Central America, according to the research team.

The study successfully connected these structural variations to crucial agricultural traits. It identified 69 genetic loci associated with fiber quality and yield, 62 of which were entirely new discoveries invisible to traditional genetic analysis.

The research also mapped specific variations controlling natural pest resistance and fiber color, and uncovered a new genetic region, VWD11, that confers resistance to the devastating Verticillium wilt disease.

Beyond specific genes, the research reconstructs the crop's evolutionary journey. The team proposes a three-stage model of domestication: originating in Mexico's Yucatan Peninsula, spreading to Guatemala, and then disseminating globally. They also demonstrated how historic natural hybridization with another cotton species introduced valuable adaptive traits into the upland cotton genome.

The work has drawn high praise from leading agricultural scientists in China. Chen Xiaoya, an academician of the Chinese Academy of Sciences, noted that the study "provides a new perspective for understanding cotton domestication and offers crucial genetic markers for accelerating biological breeding, supporting both fundamental research and the sustainable development of the cotton industry."

Zhang Xianlong, an academician of Chinese Academy of Engineering, highlighted the scale and impact of the research. "By constructing the largest and most diverse graphic pangenome for upland cotton, the team has clarified its origins and spread in the Americas," he said.

"They convincingly show that large-scale structural variations are the core driver of environmental adaptation and have provided the theoretical basis and precise tools for efficient molecular design breeding."

This genetic roadmap equips breeders with a powerful toolkit. "It transforms breeding from a broad search into a targeted engineering process," said corresponding author Li.

The findings are particularly vital for China, the world's largest cotton producer and consumer, to enhance the resilience and sustainability of its agricultural base, with significant implications for global textile security, he noted.