A multi‐parent advanced generation inter‐cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.)

Abstract

Multi-parent advanced generation inter-cross (MAGIC) populations are an emerging type of resource for dissecting the genetic structure of traits and improving breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents. These founders were genetically diverse and carried many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the United States and sub-Saharan Africa, where cowpea is vitally important in the human diet and local economies. The eight parents were inter-crossed using structured matings to ensure that the population would have balanced representation from each parent, followed by single-seed descent, resulting in 305 F recombinant inbred lines each carrying a mosaic of genome blocks contributed by all founders. This was confirmed by single nucleotide polymorphism genotyping with the Illumina Cowpea Consortium Array. These lines were on average 99.74% homozygous but also diverse in agronomic traits across environments. Quantitative trait loci (QTLs) were identified for several parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by biparental genetic mapping. The recombination events were concentrated in telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain, QTL and gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.

The genome of cowpea (Vigna unguiculata [L.] Walp.)

“…A highly fragmented draft assembly and BAC sequence assemblies of IT97K‐499‐35 were previously generated (Muñoz‐Amatriaín et al ., ). Although these resources enabled progress on cowpea genetics (Yao et al ., ; Carvalho et al ., ; Misra et al ., ; Huynh et al ., ; Lo et al ., ), they lacked the contiguity and completeness required for accurate genome annotation, detailed investigation of candidate genes or thorough genome comparisons. Here, we re‐estimated the genome size of V. unguiculata and produced a genome assembly using single‐molecule real‐time sequencing combined with optical and genetic mapping.…”

The genome of cowpea (Vigna unguiculata[L.] Walp.)

“…A highly fragmented draft assembly and BAC sequence assemblies of IT97K-499-35 were previously generated . Although these resources enabled progress on cowpea genetics (Yao et al, 2016;Carvalho et al, 2017;Misra et al, 2017;Huynh et al, 2018;Lo et al, 2018), they lacked the contiguity and completeness required for accurate genome annotation, detailed investigation of candidate genes or thorough genome comparisons. Here, we re-estimated the genome size of V. unguiculata and produced a genome assembly using single-molecule real-time sequencing combined with optical and genetic mapping.…”

Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax

“…In addition, genetic recombination is limited in these populations [14]. To increase the QTL dissection power, attempts have been made to expand the genetic diversity through other multiple-parent population types, such as nested association mapping (NAM) populations [15,16,17] and multi-parent advanced generation intercross (MAGIC) populations [18,19,20,21,22,23,24,25], while retaining the advantages of association mapping and bi-parental populations. However, the development of such populations requires careful planning and time.…”