The Hidden Inefficiency of Self-Pollination in Alfalfa Breeding.

Self-pollination in alfalfa causes severe inbreeding depression.  During alfalfa breeding synthetic seed is often produced in insect-pollinated polycrosses.  Previous work has shown that the self-pollination (selfing) rates in these polycrosses can easily be in the 30% range.  Often insect-pollinated polycross seed is grown as individual plants and evaluated in space-planted nurseries for agronomic traits such as plant vigor (i.e., proxy for biomass yield) and winter survival.  Prior to the advent of DNA-markers breeders implicitly assumed that all space plants had a common mean with a single distribution; and essentially ignored any selfed progeny.  In this study 1003 progeny of a 15 parent polycross were evaluated in a space planted-nursery from 2010 to 2012.  DNA-markers were used to determine self-pollination status of each progeny (Riday et al., 2013).  Based on the DNA-marker analysis 554 of the progeny were determined to be out-cross progeny, while 449 of the progeny were determined to be selfed progeny.  Nine visual vigor scores, two winter survival ratings, 1 spring regrowth rating, and 1 fall dormancy rating (i.e., fall growth/height) were taken over the three year period of the study.  On Average the selfed progeny clearly performed worse than the out-cross progeny.  For visual vigor scores selfed progeny were 74.8% of the outcross progeny; while for winter survival scores selfed progeny were 71.6% of outcross progeny.  Selfed progeny had inferior spring regrowth and fall dormancy ratings compared to outcross progeny performing at 79.8% and 81.6% of the outcross progeny mean respectively.  The selfed progeny performed so poorly that almost none of these individuals were considered for selection.  Essentially the selfed progeny were wasted evaluation slots representing a heretofore unconsidered inefficiency in the breeding program.  Based on this study alfalfa breeders should become aware of selfing in their crossing programs and take steps to mitigate it.  This mitigation strategy should increase selection gains by eliminating clearly inferior plants prior to the field selection/evaluation phase.