Genomics-assisted breeding——A revolutionary strategy for crop improvement

Food shortages arise more frequently owing to unpredictable crop yield losses caused by biotic and abiotic stresses. With advances in molecular biology and marker technology, a new era of molecular breeding has emerged that has greatly accelerated the pace of plant breeding. High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits. Large-scale mapping of agronomically important quantitative trait loci, gene cloning and characterization, mining of elite alleles/haplotypes, exploitation of natural variations, and genomic selection have paved the way towards genomics-assisted breeding（GAB）. With the availability of more and more informative genomic datasets, GAB would become a promising technique to expedite the breeding cycle for crop improvement.

Genomics-assisted germplasm improvement

Rice is one of the most important staple cereals,feeding over 60%of China’s population and contributes nearly 40%of the national total caloric intake（Cheng et al.2007）.A sustainable increase in rice production is required to meet the demands of increasing population and food consumption（Tilman et al.2011）.

Fast integration and accumulation of beneficial breeding alleles through an AB–NAMIC strategy in wheat

Wheat(Triticum aestivum)is among the most important staple crops for safeguarding the food security of the growing world population.To bridge the gap between genebank diversity and breeding programs,we developed an advanced backcross-nested association mapping plus inter-crossed population(AB-NAMIC)by crossing three popular wheat cultivars as recurrent founders to 20 germplasm lines from a mini core collection.Selective backcrossing combined with selection against undesirable traits and extensive crossing within and between sub-populations created new opportunities to detect unknown genes and increase the frequency of beneficial alleles in the AB-NAMIC population.We performed phenotyping of 590 AB-NAMIC lines and a natural panel of 476 cultivars for six consecutive growing seasons and genotyped these 1066 lines with a 660K SNP array.Genome-wide association studies of both panels for plant development and yield traits demonstrated improved power to detect rare alleles and loci with medium genetic effects in AB-NAMIC.Notably,genome-wide association studies in AB-NAMIC detected the candidate gene TaSWEET6-7B(TraesCS7B03G1216700),which has high homology to the rice SWEET6b gene and exerts strong effects on adaptation and yield traits.The commercial release of two derived AB-NAMIC lines attests to its direct applicability in wheat improvement.Valuable information on genome-wide association studymapping,candidate genes,and their haplotypes for breeding traits are available through WheatGAB.Our research provides an excellent framework for fast-tracking exploration and accumulation of beneficial alleles stored in genebanks.